The drive is 40GB... I have it to the point where I can boot with the Install disk but HDToolBox does not find the HD.
Try using a smaller capacity hard drive or other boot device. It will save you SO much messing around.
4gb or smaller for your boot drive. The Amiga was always limited to a 32 bit address bus. Go beyond that and you are in a world of pain.
Other possibilities are a problem with the Amiga IDE interface or cable (is it plugged in backwards?) and also, newer drives can outshoot the older interfaces. The A1200 was notorious for having an unbuffered IDE interface, not sure about the A4000 (probably is buffered, but to what extent I do not know). Although that would be down to formatting the drive on the Amiga.
You could just unplug the graphics card, setup the machine, then fit the graphics card later. Much less hit and miss.
Once you have a drive prepped, don't forget to install a boot sector via CLI to make it Amiga bootable: install dh0:
DH0: refers to the ID of the hard drive. Could be HD0: or a variety of names.
