Originally Posted by JohnZo

By way of clarification, misfire codes are being produced, but there are no actual misfires in the cylinders. The jerky motion of a lopey idle at the flywheel is picked up by the crank position sensor as timing differences between teeth of the reluctor wheel. Then the ECU logic sets the misfire codes, based on timing differences. In this case, the engine is not actually misfiring, rather the logic that sets the codes is not suited to the new cam set up at low idle RPMs.

Glad you found that the A/C idle-up was enough to get you over the hump. Perhaps there's a way to wire in a switch or jumper to make the ECU think the A/C is on all the time.