dont worry about the exhaust system, as long as everything is not plugged up your Jeep is fine, cold air intakes and headers dont help much in the Jeeps since they are already efficiently designed. What year is your Wrangler? 03-04 have the NV3550 tranny (mine) and they make a distinct "marbles in a can noise" when taking off from low gear, and they also make a weird noise at idle because they are naturally noisy truck transmissions with little insulation between you and it (only a carpet and the body). test the clutch by putting it in 5th gear, putting Ebrake on and press the gas/let clutch out, if it stalls its good if it doesnt your clutch is fried. good luck.