I'm sure that the PIO2 mod works fine with A3640@25MHz and A3660@50MHz.
Perhaps your A3640 is overclocked? Even then I think it works fine.
I think you should talk to Cosmos and maybe he can help you debug your PIO2 and/or supply some PIO0 GAL's.
http://leblogdecosmos.blogspot.com/2...00d-pio-2.html