J21,
Yes, it is safe to bore and stroke a 351 Windsor to 408. Mine is 416 and 11:1 compression. Many on the club have them bored and stroked to everything up to 427 but I would stay short of that as you are really pushing the edge there. Just make sure the block is good to start with.
As for the rest, my enjine only puts out around 515-530horse, but I have a friend with oine stroked to 410 and his puts out over 600 horse. I am pretty sure that we both have 1.6 roller rockers. I am using the aluminimun trick flow twisted heads but with a single plane intake manifold and it has all been ported and polished. I kept my power down because I drive the car a lot and it is overpowered for what I do now anyway. The top loader 4 speed could probably be improved on by having it gone through and beefier gears and such put in if you are going to make this an all out race car, which I am guessing from the engine. The suspension and rear end I will leave to the guys with Mustangs. I have a 69 Ford Torino Cobra with a big block that isn't streetable and I think that rear end is wider than the Mustang but can't say for sure. Be sure to get the 31 spline one as that only came on the high performance cars and most of the 9" rear ends were 28 spline. Pete Acala AKA Petec would be a good person to talk to as he just finished his 65 stang and sent me some pictures of him running at Sears Point. So he could tell you what all he used.
Ron