The CS MK III 060 SCSI works beautifully on mine and is very fast, so no worries there I think. If you want the onboard IDE and don't need the SCSI (IE CS Card) just use 40.68 roms. This seems to work a treat.
This was my first A4000T and I purchased it in pieces (No Case). This was driving me NUTS for a little while until I figured out some of the quirks:-D.
Keep Posted if you get any further. One more thing I discovered on mine, if you want to use a Toaster in the top video slot you can use (2)x 8 meg SIMMS in slots 1 and 3 for the onboard 16 meg instead of (4) x 4 meg simms without any problems.
Jeff