Okay so I spent about 5 hours tonight troubleshooting and eventually dropping the transmission again. I have confirmed the following:
1. The new clutch linkage is the same length as the original and the problem is definitely not in the linkage.
2. Clutch plate was installed in the proper direction.
Once I had the transmission out I had someone push in the clutch and the clutch plate slid down so the pressure plate is working properly. There was nothing obvious that was wrong. These are the two things I am wondering about
1. The input shaft on my transmission has a lot of play in it, almost 1/8". I know this is not normal, but how could this be causing my problem? Here is a link to a video.
2. The pivot point for clutch release fork is very wide. It looks like it is like this by design. I ordered a new boot for the clutch release fork, and it feels like it is forcing the fork to pivot from a position that doesn't center it in the opening of the bellhousing. Because of this, the clutch release bearing was slid out it little from the fork. I am wondering if this was causing it to now apply even pressure across the fingers on the pressure plate.
3. When installing the pilot bushing I hit it one too many times and it went about 1/16" past flush. I do know that the input shaft was going all the way into the bushing by looking at the shaft right when it came out. So I really don't think this is an issue, but I thought it was worth mentioning.