Messed up computer (10.9.4) after migration to SSD - permissions or java problem?

Question

thanks in advance for reading!  I have a doozy:  I moved my hdd to my optibay and installed a new SSD into my main hdd bay (mbp late 2011)
transferred data from hdd to ssd using superduper
so the ssd is now a clone of the old hdd (and in the same place as the old hdd) and the ssd is the startup
BUT
seems permissions are wonky?
not sure what it is.  possibly java is a problem -- maybe via permissions?
here's the symptoms:
browsers/finder work great (faster with ssd)
but MANY apps just wont load or are wonky.
bluestacks won't load-- wont even get to the "loading" animation...  (have re-installed numerous times)
metasearch on vuze won't work -- I see it for 7 seconds and then it vanishes.
other apps wont load -- the problem seems to be java related maybe?  I'm not clear.
steps I've taken to resolve:
(all did nothin)
re-installed every app that wasn't working (ug!  endless!  appcleaner etc!  hard to say how far they were uninstalled but seemed pretty thorough)
re-installed OSX 10.9.4
repaired permissions in a few ways on ssd
even "Reset Home Folder permissions and ACLs"  via rebooting with cmnd+r
downgraded to java 6 (did nothin) then back up to java 7 (nothin)
erased all the java caches etc I could find
now I'm not really sure WHAT is going on here -- but my suspicion is that there's something funny about the superduper migration and permissions  (everything was working when I upgraded to 10.9 a month ago)
I noticed: when I open a lot of folders, like utilities etc, they're read-only.  huh?  I don't think that was true, before.
to fix this I made the possible mistake of GetInfo/giving read-write privileges to everyone and "applied to enclosed items"
maybe that was dumb?
either way, after rebooting and repairing permissions, it seems the read-only structure of much of the new ssd is back
(I'm logged in as my main account as always -- is this not root? I'm never clear on root stuff...) (with mavericks, before the migration, I was able to run all these apps fine.  but none of these odd "read-only" icons were showing up in my folders)
so maybe bad permissions -- or bad java -- is the reason apps won't connect to the internet?  sometimes they crash when running animations.
ANY help would be so appreciated!  already wasted many full days on this!  ack! 

Answer 1

pingpong9 wrote:
I think another reason this might not be the best setup for me is in the comments:
>This how-to does not actually help you to create a true fusion drive. What you are actually doing is creating one volume group out of the SSD and the harddrive and presenting that to the OS as one or more logical volumes. This is a very different sort of beast than a fusion drive. With this setup, If the SSD is the first drive in the volume group, new files will be written to the SSD until it fills up and then files will be written to the harddrive. This explains why one commenter witnessed, using iostat, new files being written to the harddrive rather than the SSD and others said it started off fast and then got slower later on. If you don't want to buy a fusion drive, but do want fast boot times and fast loading of programs, I would suggest using these as two independent formatted drives. Install the OS and programs on the SSD and store the majority of your files on the harddrive.
I think I'm happy with having the SSD handling the OS etc
and my HDD doing media
wud be nice, however if when I put stuff from the HDD into the trash it doesn’t ask to delete immediately the way it would if I was on a wifi network with another volume (what IS that about...?)  these volumes are connected so directly, why cant I throw something in the .trash from the optibay-HDD and let it sit there till I'm sure to erase it?  :/
This is a Fusion Drive by definition. A Fusion drive is also a Logical Volume and a CoreStorage volume. ( Please see this as well - http://forums.macrumors.com/showthread.php?t=1530110 ). If you run the same commands on an Apple-provided "Fusion" drive, you will see similar output.
diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *256.1 GB   disk0
   1:                        EFI 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 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
diskutil cs list
CoreStorage logical volume groups (1 found)
|
+-- Logical Volume Group A8C00490-0E14-401F-AB69-59F37724E8C4
    =========================================================
    Name:         Fusion
    Status:       Online
    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)
            Conversion Progress:   -none-
            Revertible:            No
            LV Name:               Fusion HD
            Volume Name:           Fusion HD
            Content Hint:          Apple_HFS