Any fasteners that you got powdercoated or painted will have marks on them if you use just sockets on them. Worse with 6-12 pt sockets.
Here's the trick. Sandwich bags! Take a plastic sandwich bag and double it up, then put it on the bolt or over the socket.
It will chew up the bag but the bolt will look fine when your done.
Anything you polish will need something to protect it otherwise it wil oxidize or rust.
If your going to paint or clear coat you need to do it on a part that is super clean so the paint can bite well. I've tried painting two bolts. One was cleaned with Isopropyl alcohol and then painted right after and the other one I just played around with in my hands to get some fingerprint grease on it. That was enough to stop the paint from sticking well and that bolt rusted after a while.
If there is anything that is exposed metal, Like threads that are part of the frame, Use anti-sieze or heavy grease that won't just fall off. Sticky-er the better.
For bearings, Use axle grease.
Clean first to make sure there is no grit anywhere in the tube before you put the new races and bearings in the tree.
Make sure there is no overspray that will stop you from setting the bearings in place.
You can usually get them 80% of the way on by hand and the rest by tightening the top nut.
For the GRIT anywhere and in the swing arm, Spray nine, soap and water, wd40 Repeat 20 times
Keep spraying them and rotating them until you get all the grit out.
It takes time and they do come clean.
Have you tried to fit the swing arm in place? Does it still fit with the powdercoat and all the bushings?
Powdercoat does come off with paint stripper and also Permatex gasket remover.
So If you have to remove overspray it won't be hard.
I don't think the bearing on the stem be a problem. All it means is that the nut on top of the stem that holds it all together just won't be tightened down by maybe half a turn.
There's no risk of it hurting the bearings if it sits a few thow higher because of the paint.
What are you planning on doing with the seat?
Heater pads from a car seat cover fit and work nicely
All I can think of for now.