After the second transmission swap, the Midget was still making noise. It was making noise while pulling back into second. And after the car (and gear oil) heated up, it would make a rubbing/grinding noise every time the clutch was depressed. The former wasn't as big of an issue as I learned to adjust my driving habits to avoid it.
Then one day, I lost all resistance in my clutch pedal and I had a hard time bleeding it. So I went about replacing the whole hydraulic system for the clutch. This includes the master cylinder, the 5 feet of 'brake' line, a short hose, and the slave cylinder. The most difficult part was replacing the line. Since they don't sell the size thread I have on either side of the line, I had to buy the 5 feet of line and cut off an end. Slipped off the new, incorrectly sized threaded bits and slipped on the original ones. But now the end of the line that was cut off needed to be double flared like it was initially. I enlisted David's help for this portion since he had a double-flare tool (and I was too cheap to buy one). And then I rented a line bending tool so I didn't kink the line while bending the straight piece into the curvy snake it needed to be. It took some time and it doesn't look real great, but I got it all back in. I outright replaced the master cylinder with a new one, and I rebuilt the slave cylinder with a kit. I was now able to bleed the clutch system.
Then I called the fellow from whom I got the tranny and discussed the noise situation. He ended up sending me a new transmission neck (this time with an allotment for the reverse light switch!). Then I scheduled to take off of work on a Friday and drove the car to David's for transmission R/R round three. I also brought the Mini to fix a steering problem.
This time around I did most of the prep work myself before we removed the engine/tranny from the car. We got it out (which went very smooth) and assessed the situation. We put on a new pressure plate, disc and release bearing. Nothing looked drastically wrong with the old parts, though the pressure plate looked "burned" and I think there was minor wear on the thrust bearing. We also swapped on the new neck (seen in the last picture above).
Before dropping everything back in, I was adjusting the reverse light wiring when I snapped the head off of the bolt. Luckily, this area can be accessed with the transmission installed through the shifter hole inside the cockpit, so it didn't hold up the installation. A new switch is currently en route.
At this point, we also had to bleed the clutch system since I replaced the rubber hose during all of this. Once we had it bled, we started up the car. I tried shifting it into first and it wouldn't go. Even after a test drive, it was grinding real bad into first and reverse. And it was still making the noise in second gear.
We called it a day, and I returned later to pick up the car...not wanting to overstay its welcome at David's. Before doing so, David and I examined the linkage between the clutch pedal and the master cylinder. More specifically, the push rod. When David disconnected the linkage, and forced the push rod into the cylinder with a screwdriver, I was able to successfully shift. So this added travel distance (which was before limited) of the push rod enabled the pressure plate to fully disengage from the flywheel; and as a result, there was no grinding. To permanently remedy this, we removed the master cylinder and David welded an additional 3/4" or so to the push rod. So as of now, the car shifts smoothly. I'm still trying to adjust to the longer throw of the clutch pedal.
And after a couple days of driving it, I've yet to experience the horrible grinding noise from before. So hopefully that will remain the case. I still get the noise in second gear, but David has convinced me this will go away in time. It'll be 75° tomorrow, so I'm pretty excited about that!