The car is back on the road, but not at 100%. I've confirmed my 2nd gear syncro is toast. I pulled the transmission two additional times in order to fine tune the height of the clutch pivot so I don't have under or over travel of the clutch fork.
I can still drive the car since I have figured out a way to use the 1st gear syncro to get me into 2nd during a downshift from 3rd. I simply bump into the 1st gear syncro and the lever slides easily into 2nd. This is just wearing out the 1st gear syncro, but since I have to replace the 2nd anyway, I figure that is not a big deal to replace all of the syncros when I rebuild the trans.
The exhaust modifications turned out well considering my novice welding ability. I tucked both pipes up a full 2 inches from where they were so they no longer scrape on the taller speedbumps around town. The low points on the car are the bell housing and the sub frame connectors.
I have no regrets with the decision to modernize the car. While it is not as reliable as a new car, it is much better than it was in terms of drivability.