A very late update, but things have been proceeding slowly with the A3000, what with it being a nightmare to dismantle. However, it is mostly cured now, after a year of troubles.
After finding the German manual in PDF format, I found out the correct jumper settings, and removed the accelerator, to which the computer responded well. I could finally install OS 3.1.
I then reinserted the Apollo, then installed the correct 68040.library, and it ran with intermittent crashes.
The final clue? Upon ocular inspection, I noticed that the single screw holding the 3040 down was holding it in an awkward, tilted position. This is because ACT never really seemed to have the A3000 in mind when designing the 3040. While there are four holders for accelerators, just as on the A4000, the rear pair are situated far off towards the rear, presumably in order to accomodate Commodore's original cards. The 3040 only has one screw hole in the front, and that is thus the only one holding it down. The solution is to add a plate for distancing beneath the board and the screw, as well as adding some pillows under the rear portions of the card, for support. It is now held fairly well in a horizontal position.
These mechanical adjustments made the machine basically stable, but nevertheless it would give up after a certain amount of time running, after which it would lock up and refuse to restart unless left turned off for at least half an hour. Waking it up too early would result in checksum errors on the hard drive. My friends say that this is due to my old DMAC, which will overheat when stressed. I have moved the system onto an IDE drive connected to a Buddha, and the machine runs fine.
I write this update for the sake of archival, in case someone else should encounter any problems of this kind.
