Wow if not even you found a solution for the poor air circulation and heat build up....then there's no hope?
Actually I never really looked for a solution. Suspect it would probably be better with decent air circulation, etc, but that involves cutting holes and mounting fans. There's probably other solutions, but I lacked time to try things. Plus I know the Cyberstorm mk2 is running a bit hotter than it should be. As mentioned, it's only the backup computer, so doesn't get a lot of attention.
Seems you may be introducing a host of unknowns with many IDE adaptors and the likes. If you're able to, it would be worth returning the A3000 to a fairly simple, basic, state. Including a real SCSI disk with FFS. It's slow, but it does work reliably enough to prove a point.
These kinds of problems can be a real pig to track down at times. So my suggestion would be to start with as simple system configuration as possible then work your way up.
Another stupid idea; if you have a large chest freezer, run the A3000 in there to prove a point with the heating theory. The inside case temperature will end up 30-40 degrees C less than what it currently is when operating at ambient room temperature. Most disks and other consumer electronics are only rated down to 0 degC, so if you put it in the freezer and get it running within 20 minutes or so, the heat generated will keep things above the minimum operating temperature.
As an example, I'm currently soak testing a HSDSL modem outside on top of a mountain here in Antarctica. Even though ambient is -20C, I can remotely see the modem's internal temperature is +24C. It's been working happily all week so far.