I have a 97 wrangler 4.0. I recently did a "tune up" on it, changing plugs, wires, cap & rotor, and air filter. Before this I was not experiencing any issues with the jeep...just thought it was time for a tune up.
After installing/replacing the above items.... my jeep takes longer to turn over(start) when the engine is cold, probably 2-3 times longer to actually start than before... after the engine warms up, no problems... it will start right up.
Never had this problem with it before the tune up.. it would always turn over right away with no hesitation regardless of engine temperature.
I haven't yet done a tune up... but I know that the last time mine started acting up like that my CPS went out shortly afterwards... I am currently having the same issues you are, and like I said haven't done anything as far as tune up, yet... I would say just go back and check to make sure everything is tight as far as the cap, make sure it everything is installed correctly, and maybe not clocked just a little bit off from where it should be...
I know this sucks.. but take your spark plugs out one by one and double check the gap on each one. I once put some plugs back in and somehow one got mashed down on itself while I was putting it back in. Otherwise.. like the first guy said.. place each old part on one by one and try it.
"Not all who wander are lost.."
Im wondering now if its the 10% Ethenol fuel causing the hard starts for my YJ... I need to run 'er low and really look next time I fill up to get good 100% gas. Maybe run some injector cleaner through it as well. Today I cranked it over for a couple more seconds than normal and she fired right up. It always starts and runs great, just a few cranks to get 'er going. Even when warm... I had it sitting about 4 hours and tried again and still, a few extra cranks till firing up. I did my own tune up about a month ago, I previsouly had the rear plug wire popping off every once in awhile! That was pain, she'd run really rough on five cylinders!!!