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The engine came out, a new rear main seal went in, and now the clutch acts like it is slipping. It has plenty of material left, maybe it just needs to be adjusted? Can you adjust it?

Maybe the disk got contaminated with oil. The clutch itself has a wide range of adjustment over the life of the clutch.

Is it as simple as adjusting the lever on the outside of the housing? Its not oil, the clutch was well cleaned with brake cleaner

It's as simple as following the adjustment steps in your M38A1 TM 9-8014 page 231 par. 191.

If you don't have a copy lying on the tool box download one free here:
http://www.willysmjeeps.com/v2/modules. ... tit&lid=86

I have that and I already looked at that Wes. I lengthened the push rod a bit and I'll test it in the morning. I was just wondering if that was the main adjustment I needed to do. As in, will that enable the clutch to grip more tightly.

That is the only adjustment.

so, just to make sure, I lengthened the push rod, and it now has more travel before it disengages the clutch. Theoretically, should that strengthen the grip of the pressure plate on the clutch?

No.

The method for strengthening the grip of the pressure plate/flywheel on the disc is to increase the spring finger tension on the pressure plate. That procedure requires the pressure plate be out of the jeep on the table and that procedure gives you the minimum spring pressure when compressed to a certain height as given in your TM 9-8015-1. If they are too light you must get new springs. They are not adjustable.

What you did by adjusting the rod was to ensure that the pressure plate is completely released (unloaded) when the pedal returns to the up position. Before you adjusted the rod did the pedal have any free play? If there was at least 1/2" of free play then there was no pressure from the release bearing disengaging the clutch. Any clutch slippage would then be attributed to a wet clutch, a glazed pressure plate/flywheel contact surface or weak pressure plate springs.

If your real seal leak resulted in soaking of the clutch disc your best course of action while you were changing the seal would have been to replace the disc, not try cleaning it with brake cleaner.

There was freeplay. Probably to the tune of about 1/2 inch. I lengthened the rod to increase the free play to 1 1/4 inch, but aside from it softening the pedal, I don't see any difference. The clutch was fine before the engine was pulled, even with the oil leak. Now it feels like it is always slipping a little. The vehicle takes longer to speed up, and if I give it a lot of throttle, it only slowly speeds up, and I think I hear a faint grinding noise.

Try getting a borescope inside the bell through the top inspection plate and look her over. Who put the bell & engine back together?

The local auto shop by where I live. What as I looking for?

If you have no idea what to look for then it's best to have someone who does, do the looking. It would take a volume of typing to bring you up to speed on the many things to look for in there.

Ok, fair enough. Is there something the shop could have done wrong? I'm no clutch expert, but I think all they did was clean it and reattach it to the engine.

There can easily be 20 to 30 "What if they" topics. Best to get a neutral party savvy mechanic to look it over.

Having replaced many clutches...given your description it sounds like you need a new one.

Stick shifts can wear out clutches pretty fast sometimes depending on mileage, road conditions, clutch material, having a heavy foot on the clutch etc.

If you got 100,000 miles on these engines that was a lot of mileage back in the day with probably several new clutches along the way.