OP
When did the problem start?
Try swapping around the spark plug from #3 with one from another cylinder. I know they don't have much mileage, but I worked in a parts store for a bit and I know they could have been dropped and then put right back on the shelf... which could be enough for a small crack.
Outside of that, I don't have any other ideas other than sensors. They can do some weird stuff when they start to fail.
Does anyone even know what sensor trips a Cylinder 3 Misfire code? If you can figure out which one it is, I'd start there. Brief google search says maybe a Crank Position Sensor, but that was generic information and not necessarily accurate for a TJ.
Will do that tomorrow and see what happens. I'm thinking I will swap a spark plug, and then replace both cam and crank position sensors and see what happens. I guess I reached the point of throwing parts at it :/