I am about to build a pair of 36 inch wide by 6′ tall bookcases with a TV cabinet in between, and heed help choosing the finish.  I’d like to use latex  paint + water based poly (more info below) to match the rest of the room and am thinking about finishing the plywood and face frames before assembly so I can minimize runs and errors.  Never sprayed lacquer before, but maybe this is the project to start?  But then how do I match the colors?  If not, can I use woodglue on the prefinished parts, gorilla glue, or only rely on pocket hole joinery?

For background, I sprayed tongue and groove wainscott around the room  using 4 parts latex, 4 parts water based poly, 1 part flowtrol, and 1 part water — using a porter cable gravity cup conversion gun.  Ok results, but I was able to lay the boards down flat or incline them to prevent runs. 

Thanks for any guidance and help.