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I just installed a Biketronics\Sony unit on my FLHT and it was a breeze. It has a USP port for the IPOD play\sync and charges it as well. I am stumped on the best mount for it on my bars.
If your headunit has the ipod docking cable like it sounds conceal it in a windshield bag or saddlebag no need to have it out in open. Some of the Sony headunits(CDX M50IP for one) with docking cable lock out the ipod control panel when attached.