It's almost inevitable that your paint will suffer some scratches when you are doing mods, no matter how careful the shop is. And you really can't fault them unless of course something big happens. I would definitely wait till you have done at least any major mods that would require pulling the motor. You mentioned doing the heads for instance.
Fred 95 300TT SGP Stage..Who knows..lol Dynoed 539.4 RWHP, 481.2 Lbs. Torque Pump Gas @ 17 Lbs. of Boost NO NOS!!