Which SE map did you use. I have the exact same setup as you (V-mod, Filter) but am running mjw's newest map. The problem I have is the plugs still look a littl lean and this is with the stock filter. This map is richer than the SE map so I am afraid to try the others at this point.
I used the calibration file #15, can't remember the actual file number but it was for the SE slip-ons and filter.
I dynoed at Sauk Prairie HD/Buell in Sauk Prairie, Wisconsin
I just went into both VE tables and just added 10 units over the entire field on this calibration file but haven't had a chance to really drive it yet. Hopefully it warms up enough tomorrow to get some miles on it.