After trying to troubleshoot and fix this problem myself, I ended up taking it to the Mercury mechanic who was also baffled. Ended up being the prop that I put on it allowed the engine to hit the rev limiter and was causing it to miss (just barely hitting the rev limiter, not the typical sounding rev limiter miss sound). Lesson learned, don't put on the cheap aftermarket prop, even though they claim to be the same size/pitch as the factory one.