I run velocity Stack from BDM, in fact I have two, one that is straight and one that had an elbow which faces to the front. I like the one with the elbow because it give me better leg room.
You should try changing you jets to 31/76 and work from there. Being that you have short pipes you have already replaces that 29.5 some time ago. I have a 2006 Mastiff as well, but I've done a little motor work on mine and I am running a 32/76 (last time I checked). The Carb I run is a XXX TAZ which has two Thunder Jets, but they don't kick in until you go above 4500 RPMS. Bike runs great no problem with the filter in the stack.
Do a search and you'll be surprised at the information you can find and what others have done to solve Carburetor issues.
If you have it getting dyno tuned, and if they know what they are doing they should be able to adjust or re-jet you car to meet the air and fuel ratio that it need to run that filter. If they don't they suck. Good Luck.
Carlos :2thumbs: