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I just got a new 99 tj 4.0 auto and when she starts up sounds rough and back fires for a little while till I drive her for a couple minutes. Did oil change spark plug change and wires cap and rotary any ideas yall and also got a bad trans leak replaced pan gasket but cam tell where leaking from bec of wind blowing the oil
 

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It sounds to me like you need a engine diagnostic to make sure your order is correct and your spark plugs are all good. On another car of mine, I had to check the order, like four times, before I found the wires that were out of order. When all the wires are crossing, its sometimes easy to mistake exactly what wire is actually going to which plug. Might also check the gap on your spark plugs. I've got new plugs in the past and a couple of them were cracked or damaged. You could also have a leaking cylinder. One way to check that is to pull your plugs and see if there is oil around the ends of it. I'm thinking that your cylinder might be leaking and it takes awhile to burn off the oil around the spark plug once your engine gets hot. You might also check to make sure that your plugs are properly attached to the wires.
 

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Did you check the ignition coil? My was doing similar. Changed plugs, cap, rotor, wires didn't want to start afterward. but when it did run it was real rough, or back fire. Took the ignition coil off and it had about 6 cracks in it. Replaced it and problem solved!
 
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