The engine misses although with a timing light the ignition never misses? Backfiring out the exhaust although the timing stays within spec? I would agree with mrfixit that this has to be a valve issue. Sounds like an exhaust valve isn't seating- as mrfixit suggests I'd check the follower clearance, if that's within spec I'd check all the valve springs. If all looks ok there I'd suspect a faulty valve seat.