I know perfectly well that I visually scoured my SuperFX implementation 10+ times before I discovered my HIB typo.
What'd I say? What did I say?
Turns out I was clearing CY when I was clearing OV, S and Z at the start of the handler for ADD/ADC/ADDI/ADCI and SUB/SBC/SUBI/SBCI. As a result, ADC/ADCI/SBC/SBCI were behaving the same as their carry-free equivalents. That's bad.
Images, part 1/2:
Star Fox, fixes planet coloration and late culling of mothership components as it flies on-screen in the intro:
Doom, fixes everything except the massive flickering: