Sounds like it is running on 1 cylinder.-------What kind / brand of plug wires are installed ?----Wire core ?-----Is the high speed jet in the float bowl clean?----Did you have the jets ( orifice plug ) out to clean them ?
Do a complete evaluation of this vessel.-----Might be hard to find a shop to do this " patchwork " type of repair.-------You would be shocked by what a shop would charge to do a complete gut and rebuild.
As an outboard that powerhead drains itself.-----But mounted as an inboard it and the muffler need to be drained.----Look for the plugs / valve for draining it.
No need to use heat or PB blaster.--Use the correct puller.------Drill / tap those 3 holes and it should pop off.-----hopefully you have not damaged the coils.