Well Stang...you've got a couple of choices. The 2nd Gen's are pretty lean across the range, and opening up the airbox and putting a D&D can will have made it worse. Since your stutter is under hard acceleration, it is likely the needle or main circuit you are feeling.
Option #1 - get a stage one jet kit from Ivan's or Dale Walker's Holeshot. Most guys here seem to have had good luck with either. Both come with tuning instructions and support to get it working right. IIRC, Ivan's comes with new adjustable needles, where Dale uses shims.
Option #2 - You can duplicate the basics of a stage one kit by doing the following:
a) Idle/Pilot circuit - drill out the air screw plugs and set the screws at 3 to 3-1/2 turns out. This will richen the idle and up to 1/4 throttle performance.
b) Needle Jet - use one or two 0.5 mm shims under the needles. Guys have found small washer packs at Radio Shack. I have some left over (sent to me by Baz) if you want them. PM me your address. This will assist the 1/4-3/4 throttle range.
c) Main Jet - go up one (or more) size on the main jet (one of the 1200 guys could advise actual jet size) You will need to order from your dealer, or online.
If the cost is not a deal breaker, the jet kits will likely help you get it right the first time. If cost IS an issue, option 2 will likely only cost you $30 or less for the main jets, assuming you have a drill bit to remove the plugs, and if 1 shim per needle is enough. (I think I have only 6 shims to send you).