If it were mine, I would be suspecting something about my repair job to be the cause, until proven innocent. I'm sure you were careful, BUT is there any chance the timiing is off by maybe one notch on one of the pullys? Having done this job a few times, it's not hard to imagine how this could happen. And having to find TDC first adds yet another chance to go wrong. I've never had one be off a notch, and don't know exactly how it would run if it was off. I wonder if the loop closing after warm-up might be compensating for the misfire by adjusting the gas based on the full sensor input.