will try a couple of suggestions, and maybe hit on something:
There is a seal that goes between the inner and outer exhaust housing, down at the bottom of the inner housing. That could be stuck (inner exhaust housing lifts out with the powerhead, as you probably know). The kill switch wires lead back from the switch in the cowling and would need to be disconnected. The vertical control shaft (throttle) might be hanging up. There is a ground strap that goes to the screw for the rear mount (the slotted grommet) -- presumably disconnected if the screw and mount was removed.
Given how tight the powerhead remains, that pivot screw to the shift lever on the powerhead would probably be the most likely (earlier post) -- but apparently not there. Second to that, would think maybe the seal between inner and outer exhaust housing. I think you could reach that from underneath and maybe prod it a little if it's stuck.
Think six screws is right. Not sure about those rubber grommets. Two in the rear, one on the starboard side -- possible a fourth in front(?) Not sure about that lower crank seal, but sounds plausible. Maybe rocking the powerhead if you have enough separation.
But maybe in the meantime, it suddenly lifted off....