why are my marks not lining up?

What engine do you have in your Jeep? If your chain is so stretched that you can not line up all the timing marks you need a new chain and if applicable guides and tensioner. You don't want the engine timed at zero degrees before TDC but about ten degrees before TDC.

Your timing marks on the cam gear and the crank shaft gear need to line up as you say when on the compression stroke and TDC. The crank shaft balancer timing mark should line up on TDC mark off of the timing chain cover. Not uncommon if it does not. Just take note of how far it is off since you know that you are on TDC. & compensate. Time the engine to the specification listed under the hood, with a timing light. IF you are trying to set a stretched chain, it is not going to happen. Need new timing chain and gears. A stretch chain, you do not know where your at, and causes backfiring.

It's a 4.0 renix motor. When I am at tdc on compression stroke the timing mark on the crank wheel is around the 11 o clock position when the marks on the cover are at the 1 o clock position. This is what's confusing me. I can't put a timing light on it because they don't line up

Ok got ya, what you describe sounds about right. At this point disregard the mark on the timing cover. Looking at the front of the motor, your camshaft gear (sprocket) is on the upper left side of the crankshaft gear, right? (At a 11 o clock position also so to speak?) So you have # 1 piston at TDC on the compression stroke. The mark on the crankshaft gear will be at around the 11 o clock position. Now there is a mark on the camshaft gear that needs to line up with the crankshaft gear. (That would be around the 5 o clock position) When the timing chain is installed these two marks have to line up! Rotate the camshaft gear as necessary for marks to line up.....Now you are good. Just to check since you are all lined up check and see if the rotor under the cap is pointing at # spark plug wire on the distributor cap. This lets you know the distributor is installed correctly. Put it all together, Now use a timing light to time the engine. Yes that mark before starting the engine will be around the 1 o clock position, it should be by the timing tab or mark on the timing chain cover.

How you doing on this?

I am still waiting for the new timing set in the mail but thanks for the help I will let you know how this turns out

I'm having the same issue...I already got the new timing set in...dots lined up and distributor is at number 1...still runs like shit. ..was going to do a compression test but it says on the forums that it has to b in on time...so I took it apart and my chain was worn threw the tensioner so I replaced it...now it is saying codes 202 and 203 which is an open circuitous injectors 2 and 3 not sure wat that means...could it b the pick up coil inside the distributor?

I have a jeep wrangler 2.5