Last fall I went to winterize it for a friend and when I went to start it the battery was almost dead and it barely turned over

and did not start... so I turned the key to the off position (to go get a booster pack) and there was still power going to the starter relay and or starter, I could hear clicking... so I disconnected the negative terminal to stop that.   

I put a brand new battery in it and NOTHING- no crank no fuel pump pressurizing...  I put a new starter relay in and now the fuel pump works but still no crank unless I put power directly to starter cable side of stater relay.  I have tried 2 brand new relays with no luck.  The boat ran fine all summer but the almost dead battery created this no crank issue I can not figure out.  Any help would be greatly appreciated.  Thank you. 

Here's a link to your thread from last year

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=50332&KW=&title=1997-super-sport-gt40-ground-issue" rel="nofollow - link

Got the relay wired right?  See page MT16 of the link below. This is for the original PMGR starter that would be on your engine.

http://www.correctcraftfan.com/downloads/PCM_GT-40_Owners_Manual_1995-2001.pdf" rel="nofollow - link

12ish volts at the "S" terminal on the relay when the key is taken to Start?

Is the relay bolted to the engine so that it's got a good ground?

With your "jumper" installed, do you have to turn the key also or does it just start cranking?