We just bought a bought in Florida and had to pay 6% of the price of the boat. I have researched this topic for a long time now, and to be honest, you are better off paying the taxes in South Carolina because they, as far as I understand, have a $300 tax cap on used boats. In Florida, so long as you have proof that you've owned the boat outside of Fl for at least 6 months, you don't have to pay the 6% FL tax when registering your boat. SO if you ARE considering keeping it in Jacksonville, I highly recommend that you keep the boat in Charleston for at least 6 months before bringing it down, otherwise you are liable to pay the 6% and at the size of the boat you're looking at, that's a pretty high premium.
On the official SC site it states: "When purchasing a watercraft from an individual in South Carolina, you are required to pay Casual Excise Tax. The tax is 5% of the purchase price up to $6,000.00. Anything over $6,000.00 caps at $300.00 Casual Excise Tax fee. Please include this fee along with your transfer fee. If purchasing from a South Carolina permitted marine dealer taxes are collected by the dealer. If the boat and motor are purchased as a unit it is 5% of the total purchase price." Meaning that you would only have to pay $300 at most. If you need anymore information see http://www.dnr.sc.gov/boating/taxinfo.html
or feel free to PM me as I have done extensive research on this.
Also, if you DO purchase the boat in Florida, you have a 30 day grace period to get the boat out of Florida and into the state that you wish to register it in (ie-pay the taxes in). If you can't get it out of Florida for whatever reason within 30 days, you can also purchase a 180 day extension for paying the tax, so long as you remove the boat from FL within that time frame. We know because we've just missed our deadline! We originally HAD planned to move our boat to Charleston for exactly that reason, but due to unforeseen repairs, we've had to stay here
The slip fees from my research don't seem to be all that much more expensive up there...we pay around $10/ft plus $150 liveaboard fee a month at our marina here in St. Augustine.