Boot drive not found (folder with blinking ?, etc)

Question

Ok, I'll give some background. I may be misquoting some of the error messages, but I'll try to be as close as possible...
This is on a Early 2011 15" MBP running 10.9.1. Harddrive has been replaced with an SSD.
I was running low on space so I deleted a bunch of stuff - all form my home folder. Noticed that the free space wasn't there and I figured, hey, Filevault, so I rebooted to give it a chance. No problem,rebooted and there was a lot more disk space. For some reason I then decided it'd be a good idea to run Disk Utility and do a Verify on the disk. That's when the problems started.
Verify told me I should run a repair, so I did. Repair told me it can't repair the disk right now, but that I should reboot, hold down CMD+R and use the Disk Utility from THERE to do the repair.
So I did. Rebooted, CMD+R, Recovery, Disk Utility, Repair.
The Repair in there told me "Live File System Repair is not supported" or something to that effect.
So I figured I'd reboot and google that.
Only after that, I get the flashing question-mark folder.
So I figure it just forgot where the startup disk is. I power off and power back on while holding Option.
And the only option it gives me is "Internet Recovery".
I tried a whole bunch of times. Nothing. Eventually I went into Internet Recovery, ran THAT Disk Utility. That sees my drive just fine. I can double-click and enter the password tolet it access it, and I was even able to run the repair then! (it found a couple of very minor things). I ran repair permissions, too, just for good measure.
When I quit recovery it told me I might want ot choose a startup disk. Perfect! And the only one offered is my drive (even has it custom icon). I choose that and recovery tells me it's "About to boot 10.9.1 from Mr. Harddrive".
...and then I get the flashing questionmark again, and Option-boot does not show that drive. Oh, I tried resetting the PROM at some point, too.
Right now I've got that machine booted from an external drive which happens to have OS X on it. I can fully access the system drive, all the data is intact, no problems at all. But I'd still like to, you know, be able to boot from it.
Anyone have any ideas?

Answer 1

Here you go; the drive that I can't get too boot is /dev/disk3 (Mr SSD) but it looks like it's showing up as /dev/disk0 too?... I have no other 256GB drives in the system. I'm not sure why it's showing up like that and with slightly different sizes (maybe filevault?)
jethro1138@wyvern:/Users/jethro1138% diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *256.1 GB   disk0
   1:                        EFI                         209.7 MB   disk0s1
   2:          Apple_CoreStorage                         255.2 GB   disk0s2
   3:                 Apple_Boot Boot OS X               650.0 MB   disk0s3
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.0 TB     disk1
   1:                        EFI                         209.7 MB   disk1s1
   2:                  Apple_HFS Terry                   999.2 GB   disk1s2
   3:                 Apple_Boot Recovery HD             784.2 MB   disk1s3
/dev/disk2
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *500.1 GB   disk2
   1:                        EFI                         209.7 MB   disk2s1
   2:                  Apple_HFS iMovies                 499.8 GB   disk2s2
/dev/disk3
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Mr SSD                 *254.9 GB   disk3
jethro1138@wyvern:/Users/jethro1138% diskutil cs list
CoreStorage logical volume groups (1 found)
|
+-- Logical Volume Group 827A34E0-BE5D-4678-9B5A-B3DAAEA6985E
    =========================================================
    Name:         Mr SSD
    Status:       Online
    Size:         255200755712 B (255.2 GB)
    Free Space:   16777216 B (16.8 MB)
    |
    +-< Physical Volume EFB59769-CF0A-4EC5-800A-22D7F2CB88C0
    |   ----------------------------------------------------
    |   Index:    0
    |   Disk:     disk0s2
    |   Status:   Online
    |   Size:     255200755712 B (255.2 GB)
    |
    +-> Logical Volume Family 6C64D757-9450-4FFF-A0E3-B46BFBCA367B
        Encryption Status:       Unlocked
        Encryption Type:         AES-XTS
        Conversion Status:       Complete
        Conversion Direction:    -none-
        Has Encrypted Extents:   Yes
        Fully Secure:            Yes
        Passphrase Required:     Yes
        |
        +-> Logical Volume 02280DA6-34C2-4205-A4C6-28D2B8669060
            Disk:               disk3
            Status:             Online
            Size (Total):       254865207296 B (254.9 GB)
            Size (Converted):   -none-
            Revertible:         Yes (unlock and decryption required)
            LV Name:            Mr SSD
            Volume Name:        Mr SSD
            Content Hint:       Apple_HFS
jethro1138@wyvern:/Users/jethro1138% mount
/dev/disk1s2 on / (hfs, local, journaled)
devfs on /dev (devfs, local, nobrowse)
map -hosts on /net (autofs, nosuid, automounted, nobrowse)
map auto_home on /home (autofs, automounted, nobrowse)
localhost:/tQ3kz_0exBlmC1ciTfhsr0 on /Volumes/MobileBackups (mtmfs, nosuid, read-only, nobrowse)
/dev/disk2s2 on /Volumes/iMovies (hfs, local, nodev, nosuid, journaled, noowners)
/dev/disk3 on /Volumes/Mr SSD (hfs, local, journaled)