[BoxsterSteve]

You are correct in your observation that clear headlights are typically a cosmetic change and don't by themselves throw up a red flag.
A missing trunk badge by itself doesn't necessarily indicate body or paint work being done. Many owners damage them while drying the car and just pull'em off rather than replacing. It was even possible to order these cars from new with a badge delete, so that could also be the case.
Bring a buddy along with you who is a body man, and he will be able to spot telltale signs of paint and body repairs.
The easiest tell is if the paper options label is missing from the underside of the front trunk lid or the emissions diagram is missing from the underside of the rear trunk lid.

As far as mechanical stuff, odd smells and sounds tell a big story, as do a car that accelerates and tracks poorly while driving. And do check the dipstick and coolant tank for intermix and look at the oil fill location for excess vacuum and inspect the top of the engine to check for leaks too.
Best of luck in your search, looking is part of the fun!