Boat wont start, just click

We have had a lot of rain lately and I was not able to run my bildge pump so there was a bit of water in it (1996 Sport Nautique G40 PCM).  It was just barely at floor level and so I ran the pump, left, it rained some more, I came and ran the pump again, and left.  Then when I came back to crank it, it would not crank, I assumed it was probably dead so I tried to jump it and it would not start.  My battery does not sit in a battery box and I read that it should so I took the battery and hooked it up to a slow charge to bring it back up and bought a battery box for it.  Today I put the batter box in and hooked the battery up, and it still did not crank.  However, it did not even turnover, it clicked in the motor which is what it did when I thought the battery was dead.  Everything works when I hit the ignition button, but when I turn the key I just hear a clicking noise.

I do have a less than one year old starter in it, which may have been under water, could it be stuck?  I also hit the three red buttons on the back of the motor and nothing changed.

I have a new slalom ski coming Friday and my 8 year old is going to try it for the first time so I dont need this problem!

Thanks!  

When I turn the key it only clicks once per turn of the key.

I have a brand new starter from last year.  

I did not think about the relays, but how do I know which one to change?  I am going to go try to pinpoint which one is clicking, if I can, does that mean that is the one that needs changing?

I spent all day just about trying to get those two bolts out trying to get the starter off.  I had sockets with extensions, wrenches and it was bad, especially the one on the back side.  

Putting it back on, someone said, you think you can get a drill in there?  I said "no way, theres not enough room."  Sure enough, he handed me a dewalt drill and I put the two bolts in in about 10 seconds.......learned a lot if I ever have to do it again.  I bet I wont forget the bildge pump again!

A curious person would wonder why you don't have an automatic bilge pump. 

As for those manifolds.....I have never messed with them.  Last year when I took the drain plugs out of the back of them, I said "why dont I flush these out" and when I did, all kinds of gunk and rust came out of them and didn't really stop so I stopped and let them drain.  That is something I need to look at though, any suggestions?