I had a similar issue on my '06 1200 after I had V&H shortshots put on and the SE intake kit put on. It always felt like it needed to warm up more, unless it was just blistering hot outside. I think the dealer that did the install screwed me and didn't rejet the carb like they said they did. Anyways, I had it rejetted and dyno tuned and she runs like a champ now. I still have to let her get warmed up tho

 

This is normal behavior for a non warmed up 883 carb motor. I have stock jets and my bike runs fine even with an occasional carb fart which usually happen when we unnecessarily blip the throttle. Unless its under 40F my warm up is start, full choke for 15 seconds push in to half and at about a minute or minute and a half , head up the road. Once i hit 3rd i push the choke in completely. I live in the country so my take off is 0-60 and my engine is plenty warm by the time in hit slow speed city/town riding.

I got alot of carb farts at low miles but now that i have some good hard miles i don't get them much anymore.

 

You said it "had" V&H exhaust what pipes are on it now?