I have this exact problem also, just put new ES poly mounts in and it didnt help any.

I got a jethot Y-pipe and there was no way in hell it was ever going to clear the tranny brace.

 

If all else fails you could heat up the primaries before they go into the collector with a torch and bend them downwards until they clear the tranny brace.

 

well i really dont wanna do that lol

well b4 i do anything else that wastes my time i want anybody with confirmation to tell me i need to have a custom y-pipe made

the headers are already on the car and i really dont wanna take em off again ,
this may be the last time i buy jethots,

they are great headers but with these issues its retarded

/rant