Freight is a legitimate fee, as long as they only charge you what Harley charges them. Currently it is $435.00, and you can look up it up on the spec & pricing page on Harley's website.
Doc fees, dealer fees (whatever that is), and prep fees are bogus charges meant to pad the dealer's profit, and I wouldn't pay them. Harley already pays the dealer for the tiny amount of so-called prep that's required. And the profit margin at MSRP is approximately 20%, so the dealer won't exactly be losing money if he sells you the bike at the #39k MSRP. Do the math, and the gross before any other incentives, finance fees, ESP commission if you purchase one, etc. comes out around $7800. Pretty damned good profit on a motorcycle, IMHO.
Jerry