You are aware that the PSU's fan is all there is moving cool air in and then out, so replacing this with one that is far more efficient in moving air will let the case actually have cool air for the CPU to use.
Odd that there would be an accelerator card interface, a working accelerator card, stand-off posts and a CPU heat sink designed to fit the A3000 if "it was never actually a reccomended Amiga 3000 upgrade"
C'est la vie!