So it looks like maybe there's some temperature-related stuff going on?
Absolutely! However, this is in the Amiga chipset, not Indivision AGA MK3. The tricky part is data-takeover from RAM into Lisa. There's a pull-up resistor on the DRAM-A0 line of every AGA chipset, which might be worth looking at. Further, the Vbb capacitor of Alice could use some adding - I normally put an extra 10µF ceramic cap on it. C2X is on the bottom side of the A1200, so it's quire a tedious job to add that.