Flowtech hearders; mrt h-pipe, automatic?

Alright first off i'd like to apologize for not searching, im posting this in between periods...

I have an opportunity to pick up some flowtech headers, long tube or shorties for fairly cheap... which woudl you take? will they fit the factory exhaust? And whats the horsepower difference between the two...

and as for the h-pipe. I want a mrt o/r h-pipe, but after price-checking other pipes on summit i noticed alot of them said "for manual transmissions only"... with my auto how much does that limit me in headers and h-pipes.
 
If you have an automatic equipped car, it will not affect how the headers and mid-pipe bolt up. However, most headers are not designed with automatic transmission clearance in mind. Therefore, should you ever have to drop the transmission, you will have to remove the passengers side header, unless if you get a set that is designed for the automatic transmission equipped Mustangs. I believe Hooker makes a set of headers like this and one other company, but I've forgot their name.
 
The Flowtechs are the same as hooker. Dont have to remove them to drop the tranny, only problem is you'd have to use their x-pipe or have one custom fabbed for it, no others will fit it.