Windows will not boot (SSD in optibay with OSX/Window, HDD in main bay for Mac storage)

Main bay: HDD for storage (Mac-formatted)
Optibay: SSD for operating systems
Version: OSX Yosemite
Description of issue:
I removed power from internal HDD so Windows install would work properly on SSD. I didn't think/realize that once it was installed and I plugged internal HDD back in that I would not be able to boot into Windows.
This is where I am now:
Last login: Tue Apr  7 00:00:16 on ttys000
Austins-MacBook-Pro:~ austinmarti$ diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *480.1 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:          Apple_CoreStorage                         319.2 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
   4:       Microsoft Basic Data BOOTCAMP                160.0 GB   disk0s4
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.0 TB     disk1
   1:                        EFI EFI                     209.7 MB   disk1s1
   2:                  Apple_HFS 1TB Internal HDD        999.9 GB   disk1s2
/dev/disk2
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Stealth SSD            *318.9 GB   disk2
                                 Logical Volume on disk0s2
                                 98832CC2-D844-438A-BBBC-2861CCB21B35
                                 Unencrypted
Austins-MacBook-Pro:~ austinmarti$ diskutil cs list
CoreStorage logical volume groups (1 found)
|
+-- Logical Volume Group 3F0B9078-5B88-473E-8BE0-AD1B401D1B5F
    =========================================================
    Name:         Stealth SSD
    Status:       Online
    Size:         319244222464 B (319.2 GB)
    Free Space:   18907136 B (18.9 MB)
    |
    +-< Physical Volume 8B88188C-3DB7-49CB-8335-24563D7B0C9B
    |   ----------------------------------------------------
    |   Index:    0
    |   Disk:     disk0s2
    |   Status:   Online
    |   Size:     319244222464 B (319.2 GB)
    |
    +-> Logical Volume Family 53E2A31F-BA81-4969-9041-5A82D182C4F3
        Encryption Status:       Unlocked
        Encryption Type:         None
        Conversion Status:       NoConversion
        Conversion Direction:    -none-
        Has Encrypted Extents:   No
        Fully Secure:            No
        Passphrase Required:     No
        |
        +-> Logical Volume 98832CC2-D844-438A-BBBC-2861CCB21B35
            Disk:                  disk2
            Status:                Online
            Size (Total):          318872993792 B (318.9 GB)
            Conversion Progress:   -none-
            Revertible:            Yes (no decryption required)
            LV Name:               Stealth SSD
            Volume Name:           Stealth SSD
            Content Hint:          Apple_HFS
Austins-MacBook-Pro:~ austinmarti$ sudo gpt -vv -r show /dev/disk0
gpt show: /dev/disk0: mediasize=480103981056; sectorsize=512; blocks=937703088
gpt show: /dev/disk0: Suspicious MBR at sector 0
gpt show: /dev/disk0: Pri GPT at sector 1
gpt show: error: bogus map
gpt show: unable to open device '/dev/disk0': Undefined error: 0
Austins-MacBook-Pro:~ austinmarti$ sudo gpt -vv -r show /dev/disk1
gpt show: /dev/disk1: mediasize=1000204886016; sectorsize=512; blocks=1953525168
gpt show: /dev/disk1: PMBR at sector 0
gpt show: /dev/disk1: Pri GPT at sector 1
gpt show: /dev/disk1: Sec GPT at sector 1953525167
       start        size  index  contents
           0           1         PMBR
           1           1         Pri GPT header
           2          32         Pri GPT table
          34           6        
          40      409600             1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
      409640  1952853344     2  GPT part - 48465300-0000-11AA-AA11-00306543ECAC
  1953262984      262151        
  1953525135          32         Sec GPT table
  1953525167           1          Sec GPT header
Austins-MacBook-Pro:~ austinmarti$ sudo fdisk /dev/disk0
Disk: /dev/disk0 geometry: 58369/255/63 [937703088 sectors]
Signature: 0xAA55
         Starting       Ending
#: id  cyl  hd sec -  cyl  hd sec [     start -       size]
1: EE 1023 254  63 - 1023 254  63 [         1 -     409639] <Unknown ID>
2: AC 1023 254  63 - 1023 254  63 [    409640 -  623523872] <Unknown ID>
3: AB 1023 254  63 - 1023 254  63 [ 623933512 -    1269536] Darwin Boot
*4: 07 1023 254  63 - 1023 254  63 [ 625203200 -  312496128] HPFS/QNX/AUX
Austins-MacBook-Pro:~ austinmarti$ sudo fdisk /dev/disk1

I had boot camp set up previously, but I think this may have been before I installed the SSD, and maybe I just had it running on the HDD.
I've seen what seems like this same issue posted many, many times, where it is an issue of Windows seeing a GPT partition/drive, so it won't boot. Is that not what's going on for me, too?
1. I have Paragon NTFS for Mac OS X v12.2.313
2. Yes.
3. I can only see the Mac partition (but when I hold option when booting, I can choose Windows from there. Will boot if HDD unplugged) :

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       0:      GUID_partition_scheme                        *240.1 GB   disk0
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    /dev/disk2
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       0:                  Apple_HFS Mayfly                 *884.0 GB   disk2
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    |
    +-- Logical Volume Group 63DC419F-1A09-4C5B-977A-F59F79502CA1
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       Name:         FusionDrive
       Size:         888087773184 B (888.1 GB)
       Free Space:   0 B (0 B)
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       |   ----------------------------------------------------
       |   Index:    0
       |   Disk:     disk0s2
       |   Status:   Online
       |   Size:     239713435648 B (239.7 GB)
       |
       +-< Physical Volume D0BA2837-514D-4620-8E1D-26D18137CA94
       |   ----------------------------------------------------
       |   Index:    1
       |   Disk:     disk1s2
       |   Status:   Online
       |   Size:     648374337536 B (648.4 GB)
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           Encryption Status:       Unlocked
           Encryption Type:         None
           Conversion Status:       NoConversion
           Conversion Direction:    -none-
           Has Encrypted Extents:   No
           Fully Secure:            No
           Passphrase Required:     No
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               Disk:               disk2
               Status:             Online
               Size (Total):       884000030720 B (884.0 GB)
               Size (Converted):   -none-
               Revertible:         No
               LV Name:            Mayfly
               Volume Name:        Mayfly
               Content Hint:       Apple_HFS
    $  sudo gpt -r -vv show disk1
    Password:
    gpt show: disk1: mediasize=750156374016; sectorsize=512; blocks=1465149168
    gpt show: disk1: Suspicious MBR at sector 0
    gpt show: disk1: Pri GPT at sector 1
    gpt show: disk1: Sec GPT at sector 1465149167
          start        size  index  contents
              0           1         MBR
              1           1         Pri GPT header
              2          32         Pri GPT table
             34           6        
             40      409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
         409640  1266356128      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
    1266765768     1269536      3  GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
    1268035304         280        
    1268035584   197111808      4  GPT part - EBD0A0A2-B9E5-4433-87C0-68B6B72699C7
    1465147392        1743        
    1465149135          32         Sec GPT table
    1465149167           1         Sec GPT header
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    Disk: /dev/disk1     geometry: 91201/255/63 [1465149168 sectors]
    Signature: 0xAA55
             Starting       Ending
    #: id  cyl  hd sec -  cyl  hd sec [     start -       size]
    1: EE    0   0   2 - 1023 254  63 [         1 - 1268035583]     *2: 07 1023 254  63 - 1023 254  63 [1268035584 -  197111808] HPFS/QNX/AUX
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    4: 00    0   0   0 -    0   0   0 [         0 -          0] unused

    My setup is very similar to your's, Ryan, on a Mac Mini5,2 and the ordering is different and Winclone was not used.
    1. New Mini with internal 500GB with Mountain Lion(ML), put into an external FW enclosure, so the Mini can/could be booted using an external drive for contigency.
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       #:                       TYPE NAME                    SIZE       IDENTIFIER
       0:      GUID_partition_scheme                        *256.1 GB   disk0
       1:                        EFI                         209.7 MB   disk0s1
       2:          Apple_CoreStorage                         255.7 GB   disk0s2
       3:                 Apple_Boot Boot OS X               134.2 MB   disk0s3
    /dev/disk1
       #:                       TYPE NAME                    SIZE       IDENTIFIER
       0:      GUID_partition_scheme                        *1.0 TB     disk1
       1:                        EFI                         209.7 MB   disk1s1
       2:          Apple_CoreStorage                         934.5 GB   disk1s2
       3:                 Apple_Boot Boot OS X               650.0 MB   disk1s3
       4:       Microsoft Basic Data BOOTCAMP                64.9 GB    disk1s4
    /dev/disk2
       #:                       TYPE NAME                    SIZE       IDENTIFIER
       0:                  Apple_HFS Fusion HD              *1.2 TB     disk2
    /dev/disk3
       #:                       TYPE NAME                    SIZE       IDENTIFIER
       0:      GUID_partition_scheme                        *500.1 GB   disk3
       1:                        EFI                         209.7 MB   disk3s1
       2:                  Apple_HFS Rescue HD               371.8 GB   disk3s2
       3:                  Apple_HFS Leopard HD              31.9 GB    disk3s3
       4:                  Apple_HFS Snow Leopard HD         31.9 GB    disk3s4
       5:                  Apple_HFS Lion HD                 31.3 GB    disk3s5
       6:                 Apple_Boot Lion Recovery HD        650.0 MB   disk3s6
       7:                  Apple_HFS Mountain Lion HD        31.3 GB    disk3s7
       8:                 Apple_Boot Mountain Lion Recove... 650.0 MB   disk3s8
    diskutil cs list
    CoreStorage logical volume groups (1 found)
    |
    +-- Logical Volume Group A8C00490-0E14-401F-AB69-59F37724E8C4
        =========================================================
        Name:         Fusion
        Size:         1190201270272 B (1.2 TB)
        Free Space:   0 B (0 B)
        |
        +-< Physical Volume 4772013B-5520-4801-9BE5-BCAEF4AEDAB3
        |   ----------------------------------------------------
        |   Index:    0
        |   Disk:     disk0s2
        |   Status:   Online
        |   Size:     255716540416 B (255.7 GB)
        |
        +-< Physical Volume A679A101-3C78-4A59-B5EE-A4339210CFAD
        |   ----------------------------------------------------
        |   Index:    1
        |   Disk:     disk1s2
        |   Status:   Online
        |   Size:     934484729856 B (934.5 GB)
        |
        +-> Logical Volume Family 5EF5C7CA-0B9C-4169-82A1-41C84F206672
            Encryption Status:       Unlocked
            Encryption Type:         None
            Conversion Status:       NoConversion
            Conversion Direction:    -none-
            Has Encrypted Extents:   No
            Fully Secure:            No
            Passphrase Required:     No
            |
            +-> Logical Volume 1512657C-ED13-4B31-82C6-7AECBBCA7F98
                Disk:               disk2
                Status:             Online
                Size (Total):       1185508581376 B (1.2 TB)
                Size (Converted):   -none-
                Revertible:         No
                LV Name:            Fusion HD
                Volume Name:        Fusion HD
                Content Hint:       Apple_HFS
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    gpt show: disk1: mediasize=1000204886016; sectorsize=512; blocks=1953525168
    gpt show: disk1: Suspicious MBR at sector 0
    gpt show: disk1: Pri GPT at sector 1
    gpt show: disk1: Sec GPT at sector 1953525167
           start        size  index  contents
               0           1         MBR
               1           1         Pri GPT header
               2          32         Pri GPT table
              34           6        
              40      409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
          409640  1825165488      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
      1825575128     1269544      3  GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC
      1826844672   126679040      4  GPT part - EBD0A0A2-B9E5-4433-87C0-68B6B72699C7
      1953523712        1423        
      1953525135          32         Sec GPT table
      1953525167           1         Sec GPT header

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