MacBook Pro dual HDD permission problem

Alright I'm trying to summarize my problem as brief, but as detailed as possible.

I have a MacBook Pro "15 early 2011 which has a SSD in the main drive and a HDD in the optical bay. Worked fine for the past two years now I got a new logic board (known VST failure, Apple Store replacement under warranty). Now I am modifying it from the original version to the dual system like I had it before. Still same drives, besides a few weeks that went by nothing has changed about the configuration.

I can't access my HDD in the optical drive. Doing a First Aid repair in Disk Utility returns error of Node system not in place. Repairing with the fsck_hfs command in Terminal also brings an error (tried it like 25 times). I was able to format the HDD using a different Mac.

Now my 2011 model recognizes the drive but gives me the error -50 in Finder, when trying to copy files from my backup, or even creating a new folder. Repairing the disk in Disk Utility now gives the error "Unmounting unsuccessful", same error when I try to erase the disk.

Booting into recovery let's me successfully repair the permissions, but erasing still fails which now leads to the drive not being recognized again.

I checked the drive on a different Mac: Drive seems to be okay. Permissions are an obvious problem (Hint: New logic board). Backup is available, I just want to use my dual drive configuration again.

I am running OS X 10.11

Any help is appreciated.