If you are having an issue with clearing the stock brake pedal, then you do not have the engine located properly. Probably too high.
I am guessing that you may have bit off a bigger chunk than what you are able handle at this point. Mustang front end, hugger headers, engine not located properly. That is a lot.
I wish that I could help you more, but it is hard to do via communicating across fricken outer space on the Wild Wild World of Web.
All I can do is suggest that you take a step back, take a deep breathe through your nose and exhale through your mouth, and throw a tool or two.
Number one - get the engine located properly. It should be low enough so that the transmission just clears the original riveted on crossmember (assuming you have an automatic). And you should just be able fit your hand between a full sized HEI distributor and the firewall.
Number two - lose the headers and go with either ramshorns (the small ones, not the Corvette ones), or 265 manifolds. You need more room for your steering.
Carl
