I have a borla header on a 258 AND an auto trans. The problem is the shift linkage bracket that bolts to the engine and crosses over to the tub. Was not had to fabricate a new bracket. I also had trouble with the front drive shaft hitting the collector but that may have been unique to my set up. For that, I had a local shop cut off the collector weld it on facing front. Then they bent and built a new pipe that wrapped around the front of the oil pan, TJ style. I had some other work done at the same time and the entire bill was about $300, not including the header (got that from a JF member for pretty cheap.)
As for performance, I don't know that I noticed any difference. It sounds good though.
it's not nearly as close to the starter as it looks