I don't know how far you are from The Vic Shop just west of Des Moines. I would get in touch with Rylan. He could probably save you some time and unnecessary worry with a quick call or email.
The biggest thing I have learned after riding my Hammer for a couple years now, is these things don't like to be putted around. I found that if I shift at about 3000 RPM's, the popping and backfiring seems to pretty much go away. If you shift at 2600, 2700 the popping seems to happen more. Drive it like a hammer, it will love you back. I agree that the transmission is loud and clunky but it is rock solid. No problems at all. You will get used to it.
2009 Hammer - Vic Shop 116"
Hanson Racing Engines headwork - port and flow, oversize intake valves
S&S 495 cams and springs, S&S Intake, PCV, larger throttle body
Lloydz Adjustable Timing Wheel, Variable clutch, ECU, MSD coils
RPW Thor 2-1, 143HP/138TQ