What I think is happening is that some chip - possibly the RAM - starts making mistakes when it gets hot and these mistakes gets saved to the hard drive causing the loss of file associations and permissions.
Doesn't look good. Just watched a video on the disassembly of your laptop.
Looks like a lot of work. Flip it over and look at the bottom. Orient it so that the battery is at the top. You will see a vented section in the upper right. That's the fan air intake. That's where the fan and heatsink live. Doesn't look like you can get there easily. You might be able to blow air backwards through the exhaust vents while vacuuming the air intake. (Don't overrev the fan) Perhaps a cooler fan tray would help. Something like this:
I have found them at Big Lots and Marshall's for about the same price. Sometimes just propping up the back of the laptop with a book (without blocking any vents) will help with the heat flow.
You can use speedfan (previous post) to see if the tray or the book or any cleaning you do helps.