the Dyna 3000 is a black box 4 inch by 2 1/2 inch roughly sits under the seat under a plastic tray...  and the issue your having isn't timing.. its more like a vacuum leak... have you replace the exhaust at all? popping on decel is normally caused by a too lean setting.... and thats caused by aftermarket pipes allow more airflow which leans out the air /fuel mix... so the fix is to open up the PMS screws a to richen up the system... if you have a vacuum leak it can cause the same issue.. so take some carb cleaner and spray around the connections all around the carbs.. if the rpms go up you found it... if nothing happens then its the PMS screws.. everything you need is in here the bible to the 1100..

https://sites.google.com/site/vstar1100kb/home

Awesome. Thanks so much, I really appreciate the feedback.  I've had the bike for about 2 weeks and haven't made any mods to it.  I'm not sure if the previous owner modded the pipes or not..they look stock to me, but I'm just guessing.

Ill read up on the link you provided and go from there. Thanks! 

Chris

what you need to do is, take a look online at what the stock pipes look like, then make the call yah or nah.. make sure you totally understand the starting procedure ... it's different... than most others..