Upper intake manifold replacement has nothing to do with the head gaskets. You can try swapping coils and spark plugs from other cylinders To see if the misfire goes to another cylinder. But your description of coolant in spark plug hole would lead me directly to doing a compression test to check for a blown head gasket.
Depends if that's just coolant in the spark plug well after you pull out the coil or coolant on the electrode of the plug inside the cylinder. It is very common to have moisture but not so much coolant down in the plug Wells. Even ones that don't have water leaking on top of the engine can still get moisture built up down there if they're run for short trips frequently.
Sometimes all you have to do is pull the calls out and use some strong air pressure and blow out the water out of the spark plug hole and wipe off the boots and put them back on to stop a problem.
Also, when the intake manifolds start to seat or leak around either the front water crossover or the thermostat housing or any other hose that may leak a little bit the low point is going to be for the intake hits the Valley of the heads so it seeps into there and gets into the spark plugs.
Most head gasket leaks are internal anyways. The external ones typically leak on the bottom side and drip down the outside of the block and leak on the ground. Rarely will you have a head gasket leak that can get any coolant into a spark plug well. Internal head gasket Lakes allow the coolant do not stay in the small whole passages and flow through the heads. It allows them to get past the compression ring and into the cylinder and eventually fouls out the plug just due to wet coolant on it but you also slowly lose coolant from your cooling system and it will steam out the tailpipe.