On all of these the clutch goes on and comes about 1/2” from the flywheel. Nuts pull it down as they are tightened.
That's normal. You're compressing the pressure plate springs by tightening the bolts.
The trans slides in easily but stops about 1/2” from the bell housing. It pulls in when the bolts are tightened.
That's NOT normal. Measure the distance from the face of the pilot bearing area to the back end of the splines on the transmission input shaft, and also the distance from the pilot bearing face to the rear of the disk splines with the clutch installed. The second measurement should be smaller than the first, or the input shaft will force the disk into the flywheel. Have you compared the length of the splined disk hub with the clutch disk you removed? [on edit] I see that it's the original disk]
There's also a possibility that you don't have the pilot bearing deep enough in the flywheel, which would cause the bearings in the transmission to bind up when tightened that last 1/2", although that 1/2 inch should only occur on the first tranny installation, as it would tend to push the pilot bearing deeper. The second time, the transmission should be much closer to mating up with out the bolts installed. Normally, the transmission will be able to be pushed home by hand without any bolts tightened.Dragsix's comment about bellhousing alignment is especially important if you're mating a different bellhousing than what was originally on the engine. The procedure is in the shop manual, and the lateral runout limit is 0.008 inches. The bellhousing should also be within 0.010 inches of parallel to the block.
Edit: looked up flywheels and half of them had raised edges for the clutch. Looks about 1/2 inch or so. Is this what I’m looking for or should what I have be working. Really confused now.
Your flywheel should be flat across the entire back surface, but probably has a groove between the disk and the surface where the pressure plate bolts on.
