How was it running before the velocity stack?
'Don't know how you can say it's not getting enough air? Isn't that what stacks are for?
Is the idle circuit properly adjusted?
An old trick that we used to use for "tuning" the drag pipes:(2 required) weld a 1/4-20 bolt onto a flat washer (big enough to fit in the pipe(s)), drill a 1/4" hole about 12+" from the end of pipe and insert the "home made baffle" into the pipe and rotate them (adjusting backpressure) and carb settings. You just have to make sure that the "hmb" doesn't turn once you find the sweet spot.
The "hmb" works and sounds good, the last 2 bikes were a built 103 TC (SE 51mm) and a 117" Big dog (S&S carb).
+1 on the ThunderJet, 'never used one, but they do add some tuning capability to the S&S