Hard drive only bootable externally, but other hard drive is detected internally.

This is a really bizarre issue and I'm at my wits end. It all started on friday when my 2010 13" Pro was acting strange. Restarted and was greeted by a kernel panic at the apple screen. I didn't have a backup but I did have my old laptop hard drive(B) that I swapped out for a larger one back in January, anyway. I booted to recovery mode and partitioned and successfully installed yosemite onto my old drive(B) via an external enclosure and then booted to that drive(B) using option at startup. I successfully transferred all my important files off the drive(A) with the panic issue but this is when things started to go wrong.

I had simply planned to erase and format the drive(A) with the kernel panic OS X on it but when attempting that it would not unmount either via the external drive(B) disk utility or even internet recovery. I used terminal to force the unmount and then attempted a reformat and with that drive(A) I've basically been stuck at "Partition failed with the error: Wiping volume data to prevent future accidental probing failed." I can't erase it or restore to it or anything, that error for everything. So I decided to swap the old drive(B) that I had been using at my external drive and where I had backed up all my data into the macbook so I could use that till I sorted out the error. When I put that drive(B) into the computer it does not recognize that it is connected. If I attempt to let it boot normally I get the flashing folder ? logo, if hold option all I get is the internet recover option, if go to Disk Utility in internet recovery it doesn't see the drive(B). However, when I swap back in the bricked kernel panic drive(A), internet recovery sees that it is connected, I just can't get past "Partition failed with the error: Wiping volume data to prevent future accidental probing failed." However, when I attach the working drive(B) back to the external enclosure I can book into yosemite no problem, which is where I am typing this from. I'm at a loss for both issues, both the error and the non-recognition of the drive(B) by the macbook.

Short version:

Drive A has OS X on it, has kernel panic.

Attach Drive B via external enclosure.

Format and install yosemite on Drive B in external enclosure.

Transfer all files from Drive A to Drive B.

Attempt to format and reinstall OS X on Drive A via Drive B Disk Utility, Drive B recovery partition and internet recovery and endlessly get:

"Partition failed with the error: Wiping volume data to prevent future accidental probing failed."

Remove Drive A from Macbook and swap in Drive B. Macbook does not recognize that Drive B is connected internally.

Swap them back and computer recognizes Drive A internally but I can only currently run Drive B externallly.

I'm beyond stumped.