Exhaust Headers And Such

The transmission has some differences - longer input shaft which translates into a bit larger bell, and different location of the clutch fork which might interfere. The SN95 doesn't share a whole lot of sheet-metal with the Fox so there are other dimensional differences. With that said I'd once heard many Fox LT's will fit the SN95, it's the shorties that often don't. But this depends on your specific headers and how they're bent and routed, you'll want to search for information specifically about your parts.

Here's a thread discussing the issue: https://www.stangnet.com/mustang-forums/threads/difference-between-fox-and-sn95-headers.783782/