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Ok, so I finally got my clutch problem sorted out, clutch works as it should now, I get engagement about halfway off the floor now, I can put in and out of the gears while sitting still with the engine running with no problem. 1,2,3 shifts are smooth, but going into 4th I get a small amount of grinding before it drops into gear. It seems to be more pronounced after driving a couple miles and everything is warmed up. Maybe a syncro?

With the clutch releasing fully, it sounds like a syncronizer, unless the shift linkage is somehow binding.

Yes, that's what I'm thinking. I'm going to flush the fluid out of the trans and diff, just to eliminate the possibility of the problem being caused by having the wrong lube in it. Previous owner was using Redline fluid with a friction modifier in it, I've heard that can cause shifting problems with the syncros. I'll flush it with kerosene, refill with some GL-4 gear oil, see what that does.

Good idea. I went through the same situation many years ago with a Muncie 4 speed. Wouldn't downshift into first. Flushed it out and replaced the fluid - it worked great. Keep your fingers crossed!

Could also be an issue with bellhousing alignment? I had a 4 speed that would not go into fourth gear smoothly and it turned out that the bellhousing alignment was off. Since fourth gear is locking the input shaft to the main shaft, being out of alignment could cause problems there. A buddy of mine actually forgot to install the pilot bushing in his crank after switching from an automatic to a four speed. Shifted fine in other gears but grinding into fourth. He damaged the input and main shaft on that one, the small roller bearings between them could not hold the shafts in line.