Yes, the triggers on the prestolite ignitions can do some funky things, but as racerone asks, did you correct the original problem. The scored cylinder was the result - not the cause.
And NO, for 30 thou over you don't need to rejet. Going from 3.310 to 3.313" in diameter, with the same stroke of 2.8" in the cylinder, results in a miniscule increase in displacement (that cylinder started at 24.0937 cubic inches of displacement and after boring became 24.1374 cubic inches - a whopping increase of .04 cubic inches)
Before you start happily swapping ignition components (a trigger goes for over 400 bucks, the CDI box somewhat above 500) you should get it into a shop for some DV testing at different rpms to see if the components are working like they should (your manual should have the expected voltage readings for trigger, stator etc, but they can not be tested without a DV meter or a DVA adapter for a standard multi-meter). You don't want to drop a grand on a couple ignition components only to find you have a chaffed ground wire that's arcing on you...