Questions after pulling the motor and transmission

[Stainless]

The motor and manual transmission are officially out of my car, all started by me snapping an engine mount bolt in the frame. My "while I'm in there" list is growing at a rapid pace. Here are several questions and/or observances for you all:

It's clear that the motor and tranny have never been removed from the car. It was a bugger to separate the two from each other as the splines did not want to let go without a fight. I am fairly confident that my rear main seal is leaking and I plan on replacing it. My car has over 50k miles, but is easy to shift. My hunch is that I should replace the clutch, pilot bearing, etc since I have to remove them to get to the rear main seal anyway. Is that generally a good practice on a 40 year old original clutch, or would I just be throwing away money unnecessarily?
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I also discovered two numbers on my frame: one from a sticker on the back and another in the metal. For reference, my car is #2087. I'm assuming these numbers are not significant.
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I also found a lot of dirt and buildup in the rear pontoons on each side, but it was much dirtier on the passenger side. I was very surprised to see how much the bolts have eroded away, especially on a car that doesn't have much corrosion. I am planning on replacing them, but the parts manual shows M6 rivnuts here where my car has these M6 bolts, nut, and some washers. I'm wondering if my car's setup is typical or not.
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The original wrap on the wiring harness has held up extremely well for its age. There are a handful of places where it has worn through and other places where it has completely come apart, like near the alternator. Is electrical tape our best option to re-wrap, or is there something better out there? If the original wrapping is electrical tape, then it must be some really nice stuff and better than the kind I use as it doesn't seem to stand the test of time when I use it.
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The flywheel inspection plate was just loosely sitting on the frame, which I have known ever since I first crawled under the car, but now that the tranny is out, does it need to be loose, or should I reattach it before I put the motor back in the car?
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After I removed the transmission and placed it on the ground, I left it leaning a tad on one side and found a bunch of gear oil on the floor the next morning. I clearly did not drain the transmission prior to removal as it isn't that old and I didn't plan on tearing into it. I suspected that my seals around the drive flange need to be replaced. In addition to the leaks, I remembered that I snapped one of the two bolts holding on the clutch slave cylinder when I replaced it around 10 years ago. I'll be drilling that out now that I can access it and it will be more secure. Luckily, it has worked flawlessly for the past 10 years with just the one bolt holding it in place.
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I may start a new thread dedicated to just what I need to refresh the exterior of the transmission, but I will need to figure out how to clean the casing, figure out if I am going to be replacing the rusty bolts and washers, clean up all the brackets and hardware, and decide if I I want to paint it or leave it bare aluminum. Decisions, decisions. I'd love any suggestions you might have.