I agree with Militman, I have a similar setup on my 1300R and was having issues with it backfiring. So I bought that mixture screw extention from Cybrhick, got tired of tearing the bike down and fiddling with it. It kinda sounds to me like the needle may be in the wrong spot, depending on what air cleaner he has. Again, I am no expert either, just drawing from my own experience with the 1300. I personally would start by finding out what jets/needle/air cleaner you have and if nothing else post here for advice.
What I'm running:
2006 VTX1300R
Main Jet: 210
Replaced stock needle with one in the Dynojet kit(I have it clipped 3 from the top if I remember correctly, I actually had to shave off some of the back of the needle with a Dremel tool to get it back together.)
Pro-R Hypercharger
V&H BigShots(baffles removed)
Mixture screw is about 2 to 2 1/4 turns out