Sell your six and buy a GT, that's how much of a pain in the butt the "swap" and I use that term loosely, is. Put it this way, the V6 Mustang is made to use a V6, the V8 Mustangs are made to use a V8, pretty much everything (aside from the basic interior and exterior), has to be changed.
Another thing, the cost is so great actually, that unless you have a full donor car (wrecked 99-04 GT that has most of the parts you need) that you're better off, way better off, getting a supercharger and or a h/c/i from
Super Six Motorsports.
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Trinity 99 Mustang SVT Cobra 280 rwhp, 290 rwtq
Selena 95 Mustang SVO GT-40 250 rwhp, 275 rwtq (Under Reconstruction)
00 Mustang V6 (sold)
98 Mustang V6 (sold)