So I've reflowed the pins to the POKEY, SIO2PC, and RN2. Still have the same issue, however it may just need to be cleaned better.
Most of my previous issues were from bad solder joints, and some excess flux that didn't come off for whatever reason, so if that turns out to be my issue I really won't be surprised.
If I boot up without any boot interrupting settings enabled, I get the same issue. If I hold down SELECT while it boots, I get the same error message with a "[Device $00] command: $00, aux: $0000 ignored" every few clicks. It does cause some weird corruption on the U1MB Setup and other random glitches after I plug the SIO2PC in.
I tried a different cable and also my SIO2PC USB with the same results.
There was a point where the FTDI USB to Serial board had a small short which could have killed the IC on it so I'm probably going to end up replacing that soon. RN2 is seemingly fine, but from the top of the board it looks like a couple of joints need to be reflowed.
Also, I am borrowing my 800XL's IC's for now as I wait for the IC's I purchased to be shipped, so that means I'm using 1 POKEY. Just to be sure, the Left POKEY channel is the one with the PIC underneath, and not the Resistor Networks and Transistors, right?