AF Guy,
There's an old saying we use to have at the Funeral Home; "Nobody's the Same"..... the same applies to modeling.
Where there's a basic standard of building each step in the instruction sheet, one must treat each step according to the conditions, placement, fit, etc etc....
You mentioned how the paint was being messed up where the glue contacted it.... if you're painting small parts with a brush, you shouldn't paint the parts that will be bonded by glue.
The glue melts the plastic, welding the pieces together you could say... don't know about everyone else, but I prefere bonding bare plastic to bare plastic. ie: the same as scraping the chromed pieces before gluing.
Each kit calls for different applications of the SAME techniques.
I'm anal about interior detailing..... nothing looks worse than a killer interior in a sloppy finished model!
To coin a phrase from Gunnery SGT Tom Highway;
"You improvise, overcome, adapt"
Frank