I'm glad you're getting the car in tip top shape with simple maintenance, this gets cars running forever. A few years back I think mid 2017 (For some reason I just can't remember the dateL The engine was replaced by a buddy of my dad's who lived about 30 miles away. This man is a certified master mechanic with Toyota. We took the car over to him with a car dolly and after he came back from work say at 5. He did the whole engine swap that night lol! He had picked out an engine and all the parts necessary while at work, I'm not sure which exact car this came out of but it runs nice, and as of now probably has 85k miles on it, while the cars odo reads about 130k. So The next day it was ready, and it was all done right. And yes trans fluid level is important and can make a difference in shifting points and wear. Please see if you got things right in there. ChrisFix, I guess those are helpful vids, I have seen his stuff and he's grown quite a bit as a YouTube.
I did my brakes maybe 6 months ago with some nice pads, and the spongyness did go away from the previous brakes it had. But I'm getting slotted Disc rotors soon. If I were you I wouldn't put those screws in there it's totally unnecessary and most cars don't use them, especially sports cars, or expensive brake kits. Good call on using Loctite, you're doing everything right with the car down to ever point you've worked on so far.
Here what you can use instead of sanding paper man, get these at Harbor Frieght or online, mind you this cutting compound is quite strong.
And by ceramic wax coating, I don't mean like a 9h hardness ceramic kit that's like $80, unless you want to do that which is a better option. I actually meant ceramic wax, this is what I use. Works well and last a couple months before needng to add to the car again. Don't be hesitant to not be too generous with it. Use an applicator pad around the car then with a clean cloth wipe it off after it turns waxy. Make sure when applicating onto the surface to not totally rub it in way too much, as it will actually be rubbing it off, you want to have a nice layer that will soon harden before wiping it off