To the best of my knowledge, shorty headers won't work. Someone may have more info on that front than I do, I don't have first hand experience with it. As for any other headers, none were designed with a C6 in mind so I don't know if standard off the shelf headers would work either. If I had to guess, they would probably work just fine on the driver's side, but the passenger side may have problems going around the starter since I'm sure it's clocked in a different position than stock.
I've run the same Blackjack headers since the early 90s, so I haven't had to search for alternatives and don't even know what's available or not anymore. I do know that the Blackjacks aren't available anymore and the concensus is that they were the best fitting option for a stock automatic.
The only headers that would work with a C6 would be a set of Headman Swap headers all 8 Tubes go around the front Crossmember and the engine is mounted with an Engine plate mounted to the fromt of the engine!
If you have the ability to somehow fit a c6 in a mustang II (requiring a new trans tunnel among the things) then headers should be no problem to custom make. Buy a header kit and put it together the way you want it, or modify existing out of the box small block headers to fit.