@Barney
Please tell us what other specifications your A2000 has.
As for the A2091, you should be able to use up to 1Gb scsi drives with no problem with at least v6.6 version roms and could even use an earlier v6.x rom set with a smaller drive. You don't really need v7.0 roms for OS3.1.
The A2091 is still going to be a bit flaky even with v7.0 roms; the only real solution is to find and install a quite rare now GuruRom made by Ralph Babel. Since that's probably not an option, you can always help yourself by proper scsi termination, as someone already suggested.
The A2091 has two resistor packs installed next to the 50 pin scsi header on the card itself; thus the scsi chain is terminated on the card itself so you can only use internal OR external drives, but not both at the same time without first removing these resistor packs and using terminators at each end of the chain. If you're just using the a2091 for internal drives (e.g. a scsi harddisk and cdrom in the 5.25" bay) you should be okay as long as you have at least passive termination enabled on the last drive. Active terminators are better, imho, but the A2091 is a scsi-1 specification controller so you should be alright with passive.
As for the cpu, if you have a 68040 you *ARE* going to have problems with the A2091. There are DMA and other timing issues so you'd be better off with another scsi controller altogether (I'd suggest a GVP HD8+ for dma).
As for your A2000 itself, there are some subtle differences between motherboard revisions, and not just between Rev. 4 and Rev. 6, but between the myriad of release inbetween Rev. 4.1 and Rev. 6.3. There are instructions on how to upgrade each of the earlier Rev. 4.x and Rev. 6.x versions to the latest v.4.5 and v.6.3 revisions, most of which can be done with simple home soldering additions here and there an a chip replacement or two (e.g. Gary).
Hope this helps. The A2000 is one of my favorite if not favorite Amigas, partly because it was my first and partly because it's so big, easy to work on and probably had the most peripherals made for it of any machine, outside of PPC and Zorro III cards which it obviously can't use.