After much consideration, I am rethinking using my Atari 1200XL for this project. I have much restoration to do on this particular PC, and it's going to be intense, and fairly expensive. I don't like the idea of leaving my most prized possession sitting in a truck regularly. This leaves the project at a weird place.
I do have a possible solution for daily use: Atari 800XL implemented on an FPGA development board. I could stuff this into my dead Atari 400 Case and run it as a hardware emulation with working SIO port and such. I am currently working on getting the software needed to do this, before buying an FPGA board. I found this:
Getting one of those running would be quite the project for me, so I will continue to develop the software on Windows 7 with the Altirra emulator, and send programs to my 1200XL via SIO2PC adapter when I get one in. I may just do the entire project on original hardware, as planned, and use it sparingly, such as for car shows and such.