I highly doubt these headers will fit. They list them to fit the early mustang, Falcon, Maverick, etc... and the typical heders that fit these cars, definately will NOT fit a Mustang II. The Ii is extremely tight in the engine bay, and I don't think they really realize the differences between a II and the other mustangs. So I'd safely say, No, the Thorley headers won't work.
Running a C6 is really going to cause you alot more problems compared to a C4, as that C6 is quite a bit wider than a C4. Most II specific headers, designed for use with a C4 fit really tight andextremely close to the C4's oil pan. The Headmans are about the onoly one I'm aware of that provide any kind of space in the collector area that might be able to clear the extra width of the C6's trans pan. I can't be sure about Hooker's header, but I'm willing to bet that it will fit tightly to the trans aswell.
Headman and hooker both make a 'Super Comp' style header that will exit as a chassis header. The hooker requires cutting holes into the inner fenders to pass 2 tubes on each side outside the framerails on each bank. While the Headmans, all 4 tubes on each bank come out in front of and cross underneath the main crossmember. I think the headmans may or ma not require a motor mounting plate to be able to use them. If that's the case, forget about the powersteering and the alternator then.
The standard Competition headmans might be your best bet to start with but I'm sure you'll have to rework them a bit to clear that fat C6.
Bottom line- there isn't a single manufacturer out there that makes a 'shorty' style Header to fit the Mustang II V8 that I'm aware of.