This is a bit of a tricky problem: Should I put the IRQ# lines from the RTC and the UART into the control lines of the 65C22s or should I have them go into, say, a 74LVC21 that outputs direct to the IRQ# input of the microprocessor? I already have the SD detect switch go to CA1 on VIA1 but that's a special case because I'm thinking of flipping its CA1 control from positive-edge to negative-edge and vice versa depending on what the switch state is.

If you route the interrupts through the VIA's pins, you get some control of which ones are active or not, and can switch between interrupt-oriented and polling for the various devices. Sounds like a win, if you have the VIA, and enough free inputs.

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http://WilsonMinesCo.com/ lots of 6502 resources
The "second front page" is http://wilsonminesco.com/links.html .
What's an additional VIA among friends, anyhow?

Well, I had to change out a few of the discrete logic chips because they were either non-existent or didn't have a through hole version. I'll do some timing calculations and if it works out, I'll post a new thread about what I'm making in the Hardware section I guess?

Sounds great!