Andrew -
Your problem could be a rogue program running in background stealing CPU cycles which is causing your system to overheat.
Try this - Make a fresh OS install on a USB drive from the installer program. Then alter the startup disk so this drive is used. You will need to run a temp monitoring program to see if it's over heating still (running off of the USB drive). Try not to run anything off of your internal drive for this test. Is it running better?
If it is then you'll need to figure out what is chewing CPU cycles. Use Activity Monitor to see whats doing you in. At worst you'll need to reformat the drive and re-install your OS and Apps.
I would also recommend limiting File Vault just to a set of folders Vs the entire drive.