there was a thread on here just a few weeks ago about the same thing. do a search.
the outcome was basically that nearly all typical pack and ship carriers would be astronomical in price and rail shipping is not an option due to size. a hot shot shipper seemed to be the option everyone was coming up with. figure a couple hundred bucks each way, and you need to be flexible in your timeframe. the regrettable thing is that i've shipped cars, jeeps and boats across the country for a few hundred dollars--with careful planning. its not the size of the item, its the destination that costs.
if you find a cheaper and still reliable way, please let everyone know. there are plenty of folks with the same question.
as far as prep, do what Hobie does. wrap it all up with heavy duty wrap--with the seat installed. that should be enough to keep the dings off with whatever minor handling a hot shot carrier would do. just make sure to discuss with your carrier the need to not place anything on top of the boat due to the seat. and these guys are heavily insured, should anything happen.