I just installed Jackpot stainless 2/1/2 headers and Auto Tune Pro today, along with a Fuel Moto air cleaner/intake.
According to the directions, the front O2 sensor cable goes to position one.
I ran the cable for the Auto Tune itself alongside the cable for the Power Vision, in the wiring trough on the backbone of the frame.
I ran the cable for the front O2 sensor up the left hand down tube (next to the front stabilizer mount), and then into the trough. From there it was run into the fuse panel area behind the left side cover.
The rear O2 sensor was run up through an access hole in the frame just above the spark plug wires, and then snaked into the area behind the left side cover.
I velcroed the Auto Tune "box" to my alarm. Between the alarm, the Auto Tune, and the Custom Dynamics controller, plus all of the cables for the Power Vision stuff, it's getting REALLY crowded in there.
Anyway, hope this helps.
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'13 FLTRX, BBP, Vivid Black painted inner fairing, 9" Windsplitter, 14" W1 Chubbys, Get-A-Grips, Daymakers, ABS, Cruise, Security, 4 Speaker HW/Jensen HD1BT System, Fuel Moto Jackpot Header/Nightstick Exhaust, Powervision, Fueling 543 cams (95HP/104TQ). Yay, me!!