I have the same problem on my 2004 TJ 4.0.
I know it is not the injectors as I swapped cyl 1 and cly 2 injectors, and the problem stayed on cyl 1.
I replaced all the plugs, and still have the same issue.
I did a compression test, and all appears to be fine there.
I am trying to figure out where the crankshaft sensor is, to test that, but others have said in other threads that if it was the crank sensor, it would be random cyl misfires.
And other threads also stated that if the problem was with the coil, then then i would also be getting a misfire on cyl 4, since the coils fires two cyl at once.
I am wondering what your solution to this was