Help! Cylinder 3 Misfire.

Hey all,
My 02 GT 4.6 5 speed is giving me a few issues. Rough idle, sputtering through all rpms and substantial loss of power. Only addons are a magnaflow exhaust system with offroad H pipe, no cats and a cold air intake. CEL is on and it's pulling a missfire in cylinder 3 code. These are the things I've tried so far:
-plugs
-moved around coils and injectors
-cleaned MAF, IAC, PCV and throttle body
-replaced alternator
-visually checked hoses for damage.

After doing all this, I reset the CEL each time only for it to return 20 or so miles later with the same code. When I was changing the plugs, I did notice some coolant in plug wells 7 and 8 but I'm not getting any codes for those cylinders. I inspected the intake manifold and didn't see any cracks in it but I know they're prone to cracking. I went ahead and ordered a new one from American Muscle and it should be in tomorrow. I have noticed a slight tapping on the passenger side under the engine. It's hard to explain but I can even here it when I'm driving underneath the passenger floorboard. I researched that and think it may be an exhaust leak? It looks like it's dripping water on the passenger side where the exhaust turns up to go towards the engine.
The only other thing I can think of is maybe a short in the engine harness that goes to cylinder 3 coil maybe? Just trying to exhaust my resources before I actually have to go into the motor and check out the cylinder. Any help is greatly appreciated!!
 
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