As I mentioned previously, I have been having some odd problems getting the serial receive working on the MC68901. No matter what I tried, it just wouldn't work. I went into some detail in the previous log about the lengths I'd gone to to try and fix this, so I won't reiterate here. I'll just say new MC68901's I ordered from China finally arrived today, and everything now works perfectly.
Turns out my suspicion about the SI pin (or possibly RC I guess) being dead on my original 68901 was spot on, and I'm not going crazy after all.
So onward with the PCB fab! Oh, and on that note, I've just finished documenting the new board's expansion connector on Github - have a look if pinouts are your thing.