04SEDeuce,
Yes, it is a stock ECU. I am actually in decision time right now with this issue. The problem is, because our bikes come different than the regular FXSTD, they do not have a download to match our bikes when they do the Stage I (hi-flow air cleaner, pipes). The download they used for mine is 32083-01/DL. This is the download for the 1550 Race high-output motor setup.
The bike runs very good with the exception of some popping/backfiring on deceleration and sometimes when I engage the clutch at about 2500-3000 RPM's.
So, I am now in the process of making he decision between a Power Commander or HD Race Tuner (I am about 99% sure it will be the Race Tuner). I will have it dyno tuned to get rid of the popping.
Skull