After all of the work on the guts of my car, I feel the outside deserves some attention as well.

It was painted with single stage urethane and it has dulled and faded a lot especially on the roof and other top sides. Problem is a while back I had some issues due to tree sap and had to do a lot of sanding and cutting with 3M finesse it to get it shiny again back then. But it left the paint a little thin in places, so I am hoping to find something less abrasive than the Finesse It that I can use with a rotary buffer and foam pad.

Is the 3M "Perfect It" series a finer material? Or has anyone else had good results with another product?

Finesse-It or Perfect-It are the 2 things I use; actually there are no abrasives in either one. Where the paint is thin you might try a clay bar to clean it, and then wax over it.
I don't use cleaner/waxes, just straight carnauba.

If its thin and you break through there's no good way to fix it but repainting it.

I've used both for many years and find that Mequiars is a better, if not more expensive, paint polishing product. I would use the Diamond Cut Compound 2.0 with a wool pad to start with. Then go over it with No. 7 polish and a foam pad.