How about opening the bottom cover and clean out the fans and the heat sink fins using a can of can'ed air and a soft paint brush to start.
If your system is still running hot can you give us a screenshot of TG Pro window (full) so we can see whats cooking here.
You may only need a new fan, HD maybe having problems as well as your HD SATA cable.
You gave me a good clue here as Chrome is hard on drives (over Safari)
Sorry you have the classic case of worn SATA cable ;-{
What happens is the dialog between the CPU & SSD (in this case as you swapped out your HD) is breaking down. So when the CRC fails to match the block of data needs to be resent.
The best way to describe this is when you are trying to talk with a slightly deaf person and he is just getting every other word so he asks you to repeat, and repeat... At some point he manages to get what you said. But you do get hot under the collar after repeating it so many times! Thats whats happening here just bi-directionally!
You'll need to replace the cable here's the IFIXIT guide to follow: MacBook Pro 13" Unibody Late 2011 Hard Drive Cable Replacement As for the part you'll want this one: MacBook Pro 13" Unibody (Mid 2012) Hard Drive Cable - Apple P/N 923-0104 and yes I know this is the 2012 version which is a better part.
I should point out you'll want to backup your data and reformat your drive. Often when we see this problem the drive can be mis-written so you'll want to clean it off and install a fresh copy of the OS.