For those of you still talking about the various things with the clutch that could be wrong, I've had 1 mechanic friend of mine with 25+ years experience who I worked with for awhile take a look, and couldn't see anything wrong with the flyweel, clutch plate, pressure plate, throw out bearing, pilot bearing, clutch fork, and the pivot ball the clutch fork sits on, as well as the input shaft and all it's splines. All of which are in perfect condition. I also had another mechanic shop check all of this, and they even tried to install a different clutch themselves and it still didn't work. I also now have a new clutch line, and a new clutch fork since the end of the old clutch fork was a little worn down but it wasn't causing this issue.
Anyways, update on the transmission. The main input shaft bearing is shot. There is also a couple different bearings between a few gears are worn out. As well what I think was called a gear fork was out of shape. I have never done any kind of transmission work so not exactly my area of knowledge. Having it rebuilt this week and I should have a fresh clutch and transmission by the end of the week. This project car is turning into a lot more work than I ever expected, cars suck sometimes.. If that doesn't fix it, does anyone want to buy a Mustang? Fresh tranny and clutch, no test drives! Hahaha