Dean, I think your right, Fran showed me some headers for the 302, not sure if available for the taller deck blocks. I went the custom route for the headers as well (he did them), definitly cost more but are much better matched to the engine, and the heads that I had would not work with the stock style headers. The style that I did was also the more squared off versions like on the 427 motors. Fran is definitly at the PRI show in Florida this week (guessing weekend too). You should also ask him about the motor he likely has some good connections he can help with, and definitly do some searchs in the RCR section and Engine Sections you will find almost enough info to keep you busy until your car arrives!
For the 302w vs 351w debate, my guess either will fit, but a nice healthy 302/331/347 would be a better way to go, you can use the off the shelf headers, and any of them will make enough power to scare you in the GT40. The difference in doing some of the larger cube motors is that you can make big hp, and still have it not be all that undrivable. For example, I have a 347" motor that makes in the 600hp range, and would be very undriveable, one the otherhand a 427 stroker (based on a 351) with similar power might be just fine (check some of the engine threads from about a year ago you should see some comparisons on my motor and a 427 stroker). Lastly think about the transmission, that might also sway you to the small cube motors. If you have a good gear box, no matter, but if one on the edge, safer to loose some cubes. (IMO)
BTW Welcome!
Sandy