If I were in your shoes, I would dump the 4.3gb IDE drive into another computer and get a fast SCSI-2 drive to connect to your WarpEngine accelerator. It is so much faster than the hd controller on the A4000 motherboard. I have also heard of people that have removed all RAM except the CHIP RAM on their A4000D's so that the only FAST RAM was installed on the WarpEngine. This would make your system faster as well, but in my opinion, removing the mobo RAM is not really necessary as the WarpEngine will use the RAM on the accelerator card first and then the slower A4000 RAM only when you need more RAM than you have installed on the WarpEngine.
I am no expert and these are all just things I have read from others.