I have managed to enable the wait states for the VL-Bus and keep the its clock speed normal, but this didn't seem to change anything (actually, it made the drive not detect at all after that; I tried to undo that but it still wouldn't detect). I do see the on pin on the ide connector is a little crooked (the cable still fits, but the connection may be bad). However, I doubt that it would prevent it from failing detection of the drive in the bios. Also, the chipset and cpu are said to support write-back cache, but there is no option in the bios to enable/disable for this. I do happen to have some isa-only video cards, but the newest I have is an EGA card (I think my monitor can support it). I will also try to disable all cache and see if that helps, since slower speed may help. As for trying any other ide controllers, the only one I have is the one, but I do have an isa SCSI controller as mentioned in an earlier reply, but it will need an adapter for my 68-pin SCSI HDD. I will post updates soon.
Edit: Adding wait states does not change anything, I will likely try a different video card next
Edit2: Has anyone here been successful with using a network drive for booting?