I'll tell ya Zeke, with the tub out of the way, I would replace every seal at the tranny and TC, whether they were leaking or not.� Unless you know of a very recent rebuild.
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On the engine, if you remember any leaks around the pan or through the small drain hole at the bottom of the bell housing, then I would pull the oil pan.� If the oil pan is off, may as well do the rear main seal, make sure the oil pick up screen is clean, and replace the oil pan seal.� If none of these areas show any leaks, don't pull it apart.
Oil pump.� Mine have all been messy.� Pretty easy to replace the seals here, but be very careful when pulling the pump, not to change the gear position.� �
On the top of the engine, if you don't remember any leaks around the head, water pump, valve cover, don't take it apart.
Are you going to pull the fly wheel?� If so, there are a couple areas on the back side of the engine that are prone to leaks.� These are frustrating, and difficult to get to with the Willys fully assembled.
Axle, differential, pinion, yoke seals can all be replaced fairly easy with an assembled Willys, but access is a dream with the tub out of the way.� They are all inexpensive, except for the occasional Speedi-sleeve.� I would do them all now.
Running a chassis isn't very dangerous while on wheels.� I don't know that I would run through gears and such, with it up on jack stands unless I was certain that it would stay on them.
Again, I'm not trying to spend all your money, but there will never be a better time to do this.
Speaking from experience, I can think of a number of things I wish I hadn't looked past.
Tim�