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The Power Commander is supposed to mount on top of the tssm on your heritage.I have a2007 Heritage and had no problem mounting it there.Whoever told you to mount it elsewhere was wrong.
They should have discussed that with you; glad they (probably) will take care of you.
My indy had real problems finding room for my FuelPak under my '08 Fatty seat. To make things more challanging, I have the security system which makes the tray for the ECM even more shallow and left no room to piggyback a tray for the FuelPak.
My guys (after asking) relocated my Relay Tray (a.k.a. Fuse block) by unscrewing the whole thing and tucking down behind my battery in the tank well. My connectors for the FuelPak and the fuelPak itself take the real estate available after moving the fuses and relays.
Everything fits fine under the stock seat without further modification.
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Slideshow: A standard cruiser becomes an intricate metal canvas in the hands of a Swiss custom house known for pushing Harley-Davidson platforms far beyond their factory brief.
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