Running rough and backfiring

[papalode]

Summer is here and this bike is not right yet. It is an '01 FI with 18k miles. A number of events have happened since the delivery of this bike. A new battery and a loose fuel injector wire had to be reconnected. It ran but seemed to be rich at lower rpm's with some backfiring. My computer had been in the shop forever so after urging from some friends I messed with the PCIII manually. Went from bad to worse. After getting the computer and downloading the right map it wouldn't take it. The factory (dyno rep) suggested I reload the software, check the wiring, etc. After reading other posts on the pros and cons of the PCIII I disconnected it. Vance and Hines pipes and a K&N filter are on this bike. Still backfires on de-acelleration and idles on the rough side. My old carburated 99 Nomad with Vance and Hines makes this one look pretty sad. I checked for cracks in the V & H pipes and smoke tested other areas of the engine looking for a leak somewhere. Nothing. I'm at a lose as to what else to look for and reluctant to take it to the shop locally (not a great reputation) I may have compromised (unknown) the performance of the bike by giving it a shot of starting fluid early on when the starting/running issues first surfaced.
Ideas anyone? Thanks