Assuming you find a 'cheap' 03/04 Cobra motor and all the related junk you need, and assuming you're paying someone to do it (guys who know how usually don't post this question), you'll be $10,000 or more into the swap for 390 hp.
If your V6 is in good shape, you can supercharge it and make the same power for a couple grand. Do some reading in the 94-04 V6 section.
1998 Roush: M112'd Aluminum block 4.6L 2V 6 speed track car
1999 SVT: Mostly stockish
1970 Mach 1: Resto-modded monster
2000 Roush #5004 - World's FIRST M112'd V6 Mustang. Sold, but not forgotten.