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I have an 07 FXST and I do notice a difference with 6th gear compared to the others, 6th being smoother. But no real shacking at all. Bike is smooth so that doesnt sound right.
My bike is an '07 and no vibrations at all, at idle or any speed I've ridden.
As TK said, it's probably a loose mount.
As I see it, there are 2 choices: 1, walk away, or 2, lowball him and fix it. There's something wrong and it's obvious he doesn't know what it is. Take someone with you who knows what they're looking for, then offer a lot less if it's worth fixing.
I agree with Soft06. I too own an 06 standard and I have no issues with vibrations. Keep on looking. There'll be another good deal out there without the teeth chatter.