Just my two cents worth here.
I've run V&H slip ons on the stock header pipes for several months, w/o any real problems. After reading this site, I thought I needed a good tune, and increased air flow, so:
I installed the V&H true duals and a power commander and a Zipper's high flow filter. They disconnected the o2 sensors at that time. At that time they had to grind on the brake pedal lever so it didn't rub the front header pipe. I've carried the bike to two dealers and neither one could tune the bike properly. It ran like chit. Sunday at Daytona, it actually quit on me three times.
Monday I carried the bike to Zippers booth at Destination Daytona to have the ThunderMax with AutoTune installed. Of course they had to remove the power commander and re-install their o2 sensors. The bung on the rear pipe is in the wrong location. They sent me to a welding shop to have a new bung welded in. They capped the old bung.
Summary: The bike runs like a champ now. In hindsight If I knew then what I know now, I wouldn't order the V&H pipes. The front pipe hits the brake pedal. I know of some other people who have this set-up and say it didn't hit. Mine is an 07 SEUC and it hits. Then the bung on the rear pipe is in the wrong place. If I had it to do over again, I'd order a different set of header pipes. I love the auto-tune feature of the ThunderMax, as I don't have to worry about Dyno time and finding a good tuner.