Hello and welcome!
First, always a good idea to start a new thread for a new issue. That way folks will notice it better.
Not certain on the '03 models, but usually the bilge pump is back in the engine compartment, very near the center at the back (aft side) of the engine compartment. Go google bilge pump and you will see what they look like, generally. Either a little oblong block or a little cylinder looking thing.
There should be a plug at the bottom of the ski locker there. That will let the water drain from the ski locker into the bilge so it can be pumped out (or, on shore, so it can drain out the bilge plug in the back). There are probably 1 or two at the forward side of the engine compartment, too. It is a point of debate, but Yamaha says to put all the plugs in when running and take them all out when you take the boat out of the water. Downside to that is that if you get water in the ski locker (as you did), it never makes it to the bilge pump to get pumped out...
I suspect your bilge pump is not working. The way you test most definitively is to put the boat on the trailer, crank up the forward part of the boat, and fill the engine compartment with water (use a hose-it will take a lot) up to the bilge pump. It should go on and pump out a bunch. The bilge pumps have a little screen on the bottom of them that needs to be cleaned periodically, so that may be gummed up. Also, there should be a breaker (at the helm next to the switch?) and/or a fuse in the fuse box that will protect the circuit. Those may be blown (like if something got caught in the impeller and the motor overheated). Or the pump may be just dead and need replacing.
Hope that helps some.