On the racks, do not put anything between the rack and frame. You want the frame to rack connection to be as strong as possible and any kind of soft spacer would likely weaken it. When my panniers are full and I hit a rough section of road, my biggest concern is shearing off a rack bolt, but have been lucky so far. I suggest blue locktite (or similar) on rack bolts, some suggest that on fender bolts as well.

I find no need to put anything between fender stays and frame, but that connection is not one that needs to be strong. So, if you want to put something there, it probably can't hurt. If I had a paint job that cost over a month of income, I might be tempted to use a stainless steel washer between fender stay and frame.

I however did put several layers of electrical tape on my kickstand before installing it on the frame to protect the paint. Others have used inner tube rubber for this purpose instead.

I have no experience with any trailer hitches and therefore can't comment.