Well, I think I have this about figured out. When using the CS MKII you leave the jumpers the same as they were/are for the internal 030/25. If you are going to use an A3640, then there are 3 jumpers that need changed. If I had started with the stock configuration and installed the MKII, I would have been fine. I was starting with the jumpers configured for the a3640.
A3640
J100 = 3-4
J102 = 2-3
J103 = 1-2
J104 = 2-3
CS MKII
J100 = 1-2
J102 = 2-3
J103 = 3-4
J104 = 1-2