I have almost the same problem as you. I´m trying to get my WarpEngine to work in my A3KD too, the problem for me is that it crashes after 4-5minutes and doesn´t work until I turn the computer off and on.
What I have done first of all:
Copied the WarpEngine 040 library to the harddisk.
Fixed the jumpers to the right positions: J100=3-4, J102=1-2, J104=1-2 (The org. A3K settings are: J100=1-2, J102=2-3, J104=1-2)
After that it works 4-5 minutes until it crashes into Gurumeditation and does that until I turn the power off.
My motherboard has the INT2 already so I don´t use the cable.
I have a Zipp2Simm converter too.