No specific answer for you, just an observation: my MkII would get quite hot, particularly on the bottom, after being used at home, plugged into the wall. My new MkIIa seems to be just fine (which is good, as it's plugged in all the time and hooked to my home stereo).

What's the difference? Well, my MkII has two drives, where the MkIIa has one. This causes the IDE cable to be pushed up against the top of the MkII, leaving less room for air to flow out the top airholes.

In-car, of course, is a completely different ballgame...