It's not my fault I have old information, I just can't find much info on the controller hardware, especially the expansion port. But thanks for answering my question.
I don't really want to use the expansion port because i tend to make unstable connections, and i'd be a hassle to hook up wires. In the case of using a controller, I could just plug it in and use it.
I think what I'll do is have monodirectional transfers (ick):
Strobe -> Pin 10
D0 <- Pin 2
D3 <- Pin 5
D4 <- Pin 6
The PC would send a Clocking pulse on D4, and data to the NES on D0+D3. This would actually make the protocol I was thinking of go faster, and since the timing is sent from the PC, it probably will not fall out of Sync (since the NES only has to process the incomming information).
I'll build a web site soon so that I can put up sources and whatnot. The only issue I have is that I do not have any sort of EPROM burner, so I cannot make fesable chips to replace the old ROM.