How should I go about the closing process? Should I just hand the marina a check for the full offer price with the "contingent upon survey" statement? Do I need to draw up some kind of contract for the contingency? Any advice or anecdote from similar experience would be very helpful.
While others have opined on your plan, only a few answered your question.
It is standard practice and a good idea to have a written offer. Include in the offer the conditions of the sale and the conditions under which you will not be obligated to follow through on the deal. A refundable deposit of about 10% should be paid when the offer is made. Both parties sign the offer.
Minimal conditions should include:
The seller provides a clear title and indicates the boat is free of any liens.
Survey results are acceptable to the buyer.
A sea trial to ensure the engine and all systems operate. I don't think it is necessary to actually sail the boat, just put it in the water, run the engine awhile, check for leaks etc.
Sometimes there is a holdback clause in the purchase offer to cover repairs to the engine or unforeseen damage after the sale is complete. The seller is usually anxious to get the holdback, so there will be pressure to get the boat in the water.
Once the survey is back and any issues are addressed, a bill of sale is signed and money exchanged. States differ in how they collect sales tax. In NY if the boat is sold through a broker, the broker is required to collect the sales tax. However it is collected, it will have to be paid in order to register the boat.
As for your plans, be prepared to spend more than you planned and for jobs to take longer than you think. Keep a good supply of band aides and ibuprofen on hand.
http://www.sv-secondstar.net/blog/second-star/16-there-ought-to-be-a-law
A couple Youtube channels to watch are
Sailing Uma and
White Spot Pirates, both channels document the trials and tribulations of a plan such as yours as well as the joys and successes.