We had a similar problem on our 500DA. We checked everything but the lint filter. Once we cleaned that, and it had loaded up from towels, it worked perfectly again. It may be as simple an issue as was ours...
I had a similar issue a number of tears ago on our '96 450DA. I pulled the manual for the unit, found the mfg. phone number, called and explained the issue, and they sent me the parts and replacement instructions gratis. Hope you have a similar exp...
I had the same issue with the discharge hose of my bilge pump on my 2000 500DA, which wasn't looped, providing an easy entry of sea water through that scupper while underway. Sea Ray, with apologies, had added a loop and check valve through our deal...