Start with large thin panels - these are most likely to pick up vibrations and turn them into noise, the thicker structural beams far less so. So the firewall is the prime contender - basically a thin panel with a large noisy thing on the other side.
I'm guessing that on an old 'stang the door panels' exterior skins will need it too. (Many modern cars have safety beams that effectively cut the panels into multiple smaller panels).
The third large area that should also be done is the floor pan. Although probably thicker than the door skins, most of it is not 'structurally strong' and will pick up vibrations given it's large area. Should help with road noise.
Roof panel (if not convertible) is also a prime candidate.
After that, the remaining problem areas are likely to be car specific, 'stang forums may have a handle on known contenders. Otherwise it's going to be a case of cranking up the volume and locating the buzzes and rattles.

I'd suggest that RTA isn't going to be amazingly useful in this task. Sure it will show the peaks of the resonances due to panel vibration, and also the lack of those peaks after those panels have been damped. However, it's also going to show peaks and troughs arising from elements that you aren't going to be correcting with dynamat, eg window vibrations, seat absorbtion, basic car geometry etc, which could just confuse the issue.