Thanks everyone. So the linkage issue definitely muddied the waters. At the beginning, when I would come to a stop in gear with the clutch in I didn't feel the car trying to pull forward when I let off the brakes which is why I thought it was a linkage alignment issue and not a clutch/flywheel issue. After maybe 300 miles I could tell something wasn't right because I could feel the clutch and flywheel chattering and starting to make contact even with the clutch all the way in. It then continued to get worse until the clutch wouldn't disengage at all.

It sounds like if I added a couple mm to the slave cylinder rod it may fix the issue and I shouldn't be risking damaging anything by trying it.

I should add that I have the metal USP cylinder, their braided lines, and have put in a new master clutch cylinder so that side of things should be good, and it does feel completely solid now that the slave is out of the transmission and bottomed out.