I've got Hooker Supercomps 2 1/8" primaries with 3 1/2" collectors and 3 1/2" exhaust from the collectors via X-pipe and through the gravelshield. They do their job, but I am not big fan of the headers when they go under the lower control arms as this ones does.
I would try Ford Power Train Applications tri-y shorties for 429/460. My friends 514 cid Mustang has them, no complains and huge ground clearence.
http://www.fordpowertrain.com/FPAindex/Mustang1.htm
Remember that the 1 7/8" primaries headers can support plenty of hp. Take a look at this chart if you haven't visited www.460ford.com pages earlyer:
http://www.460ford.com/forum/showthread.php?t=119213
Anyway, good luck with your 460 project. One of the big reasons why I am not owning and driving a '69 Mustang SR/Mach1 is due to it was planned for FE and '71-'73 was made wide enough to accommodate the 429 (even the boss 429). I wanted a Mustang that I don't have to chop the shock towers in the first place to make room for the 429/460 cid engine. Now years later I would gladly get rid of the shock towers but I am still glad that I ended up with the big pony.