So all the things that went wrong immediately after disassembly...
1) I realized that the transmission I had didn't come with the necessary brackets and they would need to be ordered from the dealer (three day delay)
2) I banged the rear oil seal in too far and needed to order a new one along with the brackets.
3) I destroyed a wheel bearing while getting the axle out. I ordered the replacement parts from Amazon, but they were stolen from outside my door (additional 3 day delay).
4) Lost one pressure plate bolt and washer after replacing the rear main seal... Another dealer order
5) Finally, I was sold an obviously broken clutch pedal by Harbor Used Auto Parts in Lynn, MA. Luckily, I was saved by a forum member.
I was lucky that the lift was open this whole time. There was very little I could do while waiting for parts. If I did more prep work, I wouldn't have run into these problems. Eventually I replaced the wheel bearing and rear main seal. I banged the rear main seal in way too far. I had to rip off the inner annulus of the RMS and pull the circular spring out. Eventually, I used two self tapping screws to get the rear main seal out. After the pressure plate bolts came in, I was able to speed up reassembly. My roommate helped me out a lot. My girlfriend brought me food at the shop and drove me around a couple of times to pick up parts.