No - no GT mid-pipe will work with V6 headers. The BBK shorties are just replacements for stock, so they go to the same location and attach to the midpipe the same way. If you got long-tube headers, they would require yet another style of mid-pipe...
If you want dual exhaust, you have a few options: (I'm assuming you still have the stock Y-pipe, just different headers)
1) divorced duals: either cut after your cats and add straight tubing to mufflers, or just use straight tubing & mufflers (if no emissions)
2) adapter pipe: couple places sell a "H-pipe" style adapter specifically for V6s. You just cut your Y-pipe after the cats and before the merge, add the adapter, and then attach an GT (V8) catback exhaust to it.
3) V6 specific system: either a full system (midpipe, mufflers, tailpipes) or catback system (reverse Y-pipe, mufflers, tailpipes) are available. Obviously the full system is better for power & flow, but the catbacks will get you a decent sound.
I can expand on any of these subjects, so just ask if you have more questions. :wavey
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