It's getting harder to be confident in marking my own work. I've adopted a multiple pass technique that seems reliable so far. I'll edit this post if I end up changing my approach.
First pass: check for fifths, eighths, and unisons on the first beat, and make sure they're entered via contrary motion. (I'm especially prone to error when entering the penultimate bar.)
Second pass: scan through for bs and fs. They're always dissonant against each other, so double check any b-f harmonies. Also check for exposed tritones in the counterpoint any time a b or f appears at the peak or trough of a melodic run. If the counterpoint uses any accidentals (for example, in the closing formula) run the same set of tritone leap/exposed tritone checks on the accidental.
Third pass: locate all dissonances, and double check that they are entered and left stepwise, or are part of a cambiata formula.
Fourth pass: scan through the counterpoint and note every jump larger than a fifth. Double check that none of those leaps are forbidden. Also double check that any leap larger than a fifth is "recovered."