I have that same problem. first let me state that iv got the V&H twin slash , the Cobra Power Flo intake, and the Cobra PowrPro AutoTuner - and the bike was doing this only in the 2nd gear cruising at 35mph... Well I took off the PowrPro and sent it in to be fixed / reparied.
I ran the bike and it got worse without the tuner - now experiencing it in 1st gear and 2nd gear like you... So, I unplugged the O2 sensor from the bike and while it still stutters / chuggs / surges - it's no where near as bad as when the sensor was plugged in.
So, I'm hoping that when I get my Tuner back - it will solve those little nagging issues, - I'll leave an update when I know more.