First, I'm sure you googled the heck out of this. But there is a clue in your post. It's a slim one.
" keeping the home folder and every other file apart from system and apps on the HDD. "
I wonder what would happen if you clean installed the OS X and used the folders as supplied without tinkering, worrying about what goes where.
I just installed a Samsung SSD 840 EVO in the optical bay of my 13" Macbook Pro (mid 2012). Now I'm running OS X 10.10.4 on the SSD, keeping the home folder and every other file apart from system and apps on the HDD.
Now, when I try to transfer files (generally large files) from the SSD to the HDD or an external hard drive, most of the times it gives me this error at some point during the transfer:
The Finder can’t complete the operation because some data in “File Name” can’t be read or written.
(Error code -36)
Sometimes it happens after a few MBs, sometimes almost at the end of the transfer, sometimes (rarely) it works fine.
Note that I have no problem writing data onto the SSD from any drive, so the problem is only transferring data from it. Also the drive does not seem to give me any other problem. It works as fast as it should and I can open any application from it.
I just updated to 10.10.4 and enabled TRIM to see whether that could be the problem, but it did not solve it. I also tried the "dot_clean" solution that has been suggested elsewhere for Error 36, but it didn't work either.