I have no experience with the Apollo boards, but getting an accelerator to boot from either a warp engine 3040 or a cyberstorm mk III couldn't be any simpler. Just put a drive on it and go to the info of hd toolbox and add in the scsi.device. The int2 wire needs to be soldered in for the cyberstorm but not the warp engine (they have a special clasp to attach directly to the CIA legs).
It sounds like this is very specific to the Apollo board, as I doubt that the kickstart would have any bearing on this.
The only issue that I can think of is bad termination, that some early boards had.
