I always paint the body after I get a rolling chassis, I KNOW is going to fit under everything.
Including interior, glass,tires and wheels of choice etc.,
There is nothing more aggravating to me than getting to final, and having to pull out the dremel on a polished body!
Even without body mods I test fit, test fit, test fit.
As far as window trim,...after paint and polish,... I will use a sharpie for black or BMF