@drbytes,
What version were the original ROMs on the A3000?
Try reading some of the archived newsgroup messages about rom problems. Some of the solutions might work out for you. (
link).
I vaguely remember reading about occasional compatibility problems with rom towers and 3.1 roms. The solution was to try a different set of 3.1 roms. I'm on my way out right now and I couldn't find the original links regarding this issue. Perhaps I've jolted somebody else's memory and they can step up?
Edit: From reading, it looks like there might have been two different versions of the 3.1 ROM out there. One set was for systems without a rom tower (such as rev 9 motherboard). You could also use it with a rom tower on an older motherboard, if it worked for you. If it did not work, then you had to get the special version that was for systems with a rom tower. Except, you didn't use the rom tower. The roms were programmed differently to compensate for what the rom tower did. I also read some issues with getting them to work with 16mhz, and some issues getting them to work at 25mhz.
At this point, your best bet is to contact a reliable Amiga vendor such as AmigaKit or SoftHut (or others, but those are the only two I remember). Explain to them your problem, and see what rom kit they recommend. That way you are sure to get what you need, and some assistance if you run into further problems.
Good luck!
-David