about 3 inches or so after the collector flange on my drivers side header, jethot longtubes, the trans cross brace dips about a half or full inch in to the way... just wondering how the exhaust system is routed normally, does it just take a severe curve around the brace or what?

 

Its not that severe, and a good pipe bender should be able to take care of it.
This is with a true dual setup going into an X pipe.
I have a guy installing mine soon and we talked about this already.