New starter body is making contact with flywheel

That sounds like the new starter may have different housing dimensions. Mic the old and the new one and check. I'd return it for swap.
 
I ordered a new one from extreme terrain. Specs for a 06 Jeep Wrangler 2.4L. Doing the exact thing as the one from auto zone.

The starters changed through the years I believe. If I had to guess, the one you ordered is for a 4.0 possibly.

Can you post a link to the exact starter you ordered?
 
56041436AC - Starter for 2006 2.4L

56041012AE - Starter for 2006, 4.0L, with manual transmission

56041914AC - Starter for 2006, 4.0L, with automatic transmission
 
The starters changed through the years I believe. If I had to guess, the one you ordered is for a 4.0 possibly.

Can you post a link to the exact starter you ordered?
56041436AC - Starter for 2006 2.4L

56041012AE - Starter for 2006, 4.0L, with manual transmission

56041914AC - Starter for 2006, 4.0L, with automatic transmission
Crown Automotive 56041436AC

1592674681575.jpeg
 
How do you know it’s the body hitting the flywheel and not worn ring gear teeth? Remove whatever starter you have installed and look at your flywheel for damaged ring gear teeth. You will have to turn the engine several times to inspect all the teeth.
 
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How do you know it’s the body hitting the flywheel and not worn ring gear teeth? Remove whatever starter you have installed and look at your flywheel for damaged ring gear teeth. You will have to turn the engine several times to inspect all the teeth.
It’s a possibility. I’ll check because turning the Engine by hand it seems to catch in one particular place.
 
Flywheels are actually surprisingly inexpensive on RockAuto. Pick up a Luk clutch kit and do the clutch and bearings at the same time.

The expensive part is if you pay someone else to do the labor. DIY, it takes about 15 hours
 
I’m seriously thinking that a bolt on the flywheel is loose or come completely out. I’m going to drop the transmission and take the flywheel completely off and have it resurfaced also.
 
I’m seriously thinking that a bolt on the flywheel is loose or come completely out. I’m going to drop the transmission and take the flywheel completely off and have it resurfaced also.
You don't want to have the flywheel resurfaced. The FSM specifically warns against it. The flywheel has a slight conical shape (can't remember if it's convex or concave) to make clutch engagement smoother. Resurfacing will eliminate that feature.

If it does look damaged, simply replace it. I've seen new ones for as little as $60. You might be able to find a good used one somewhere. I upgraded to a much more expensive high inertia flywheel (Centerforce) when I did mine, but that is far from necessary.

I believe 91-04 flywheels are all interchangeable. 91-04 flywheels cannot be interchanged with 05-06 flywheels due to sensor clocking (05-06 has three but 97-04 has two IIRC).

The clutch kit runs about $80 and you have to disassemble the clutch to get to the flywheel, so you might as well replace that at the same time. The kit comes with a throwout bearing and a pilot bearing, though most upgrade to a different throwout bearing.

Consider buying ARP flywheel bolts. They have the same profile as the factory bolts, but are made from a much stronger alloy. If you add a heavier flywheel or go to a stroker/supercharger/turbocharger, they are highly recommended to reduce the odds of having a flywheel liberate itself from the crankshaft.
 
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