I have a stage 1 A/C on my Dyna. I did have a Thunderheader 1031 exhaust. I put the stock pipes back on, and I noticed that it was running a little ruff. This morning my 6 year old daughter and I marked off the with painters tap the throttle %, and I put the VCI on the bike. Loaded the stage 1 map, and went to a 2 mile straight away by my house. Did the runs for about an hour. Yes, they say 15 minutes, but the device actually records closer to an hour of data.
Came home loaded up the stage 1 map, downloaded the recordings, and used the smart tune to update my map for putting the stock pipes back on while using the open A/C.
After I got the VE corrected, I set all the fields in the CLB to 700, and loaded the map. I went for a 50 mile ride that included interstate, state parks, hills, twisties, and long straights. The bike performed a lot better, ran cool, and did not surge, sputter, dodge, duck, dip, dive, or dodge.
I will do a couple around town recordings to add to the mix. It should fine tune it a little more to the way I ride.

I noticed something while the throttle % is tapped off on my bike. Doesn't matter what gear I am in. I stay right around 6% throttle. On the interstate I might run 12% in 6th gear for 75-78 mph. Thought I'd share that last little bit of info for you.

Also if you read the SEPST manual. You can tune your bike to run in open loop, and get the most HP and Torque out of it, but for a good solid commuter the closed loop features work perfect.

I don't know what the orange SEPST is all about. There is a thread saying that it will not allow you to edit maps. Don't know about all that. I don't have experience with it, but if you can get the one I have. You will be pleased. It will tune your bike.