Have you checked the plugs themselves? Swapped injectors (I assume not all cylinders are misfiring) to see if the misfire moves cylinders? Done a compression/leak back test to ensure it's not a leaky valve?
Seems like there's lots of possibilities we haven't yet explored, unless you just haven't mentioned them.
'06 Jeep Wrangler, 65th Edition, stock.
'98 Jeep Wrangler, stock.