IMO:
1. The OE hoods on these cars were notorious for not fitting well and "bowing" in the middle from the hood hinge springs. If the (assuming) steel hood fits nice and your T/A one doesn't then adding fiberglass I think would be the best choice. You might also consider getting a new hood from a decent fiberglass place. It may cost you less in the long run if the painter can just scuff, prime and paint as opposed to building up the fiberglass on the current hood to fit the car. If your current hood is a factory hood, you could sell it to someone doing a restoration to help offset the cost of a new hood since you are building a clone.
2. What color is your car? Is it metallic? Is the current paint job relatively new? Hopefully, if the car was repainted, you have a sample of the paint used or the brand. It is going to be tough to match up just the fenders (if they paint the whole fender) to an existing paintjob unless the painter does a "blend" (transition) into the door area. Metallics are the worst to match up. If possible, maybe they can paint just the tops of the fenders since that is where the repairs will be made since there isn't really much area right next to it that you can see in the same "light" from the same angle/plane, just the top of the door which is a pretty small area.