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I drive a 99 wrangler and am having similar problems. The other day leaving school I could hear a loud ticking noise sounding like it was coming from the engine. Took of the valve covers and checked the valve springs, rocker arms, and push rods, couldn't find the problem. Then I borrowed a tool called an ear and found out that it was coming from my transmission. You most likely have the AX15 transmission same as me. I suggest lifting it, and verifying that the sound is coming through the transmission then take of your starter and inspection plate

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Q: Your 98 Jeep Wrangler Makes clicking noise while driving even worse when clutch is engaged Sound is either coming from clutch or transmission. Please help shed some light on this problem?
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