Detergent, water, and a LOT of elbow grease!
Your story brings back memories of what my last boat smelled like when I bought her--a wet bilge that hadn't cleaned in at least 5 years, permeated sanitation hoses, mildewed lockers and softgoods (carpet and upholstery) that not only stank but had stains I didn't even want to speculate about. First, toss all the cushions, any carpets and or rugs, life jackets and everything else that's loose off the boat. Then either grab a scrub brush, a bucket, several gallons of Raritan B.C. and start scrubbing...better yet, borrow or buy a power washer--1200 psi at Home Depot is about $200 and worth every penny IMO...I use it at home too..don't know how I ever got along without one. Aside from the dry rot, the bilge, chain locker and any sumps are your main odor culprits...followed closely by lockers and sanitation hose. Once you get the boat clean--really CLEAN--it'll be a lot easier to pinpoint the other sources. The key to really clean bilges, chain locker and sumps is a LOT of detergent, followed by rinsing ALL the dirty water out. A real advantage to using a power washer is its ability to clean and then rinse out places you can't reach. Once you get it all clean, use a hand pump, sponge bucket to remove the water the bilge pumps leave behind...your objective is a dry bilge. So leave hatches open so that plenty of fresh air can circulate for at least a day. Lockers are next. Since they're likely to be full of mildew, Clorox Cleanup is a good choice for scrubbing 'em all out. Again, leave all the doors and hatches open for a day. Now you'll be able to tell what else still stinks--sanitation hoses, dry rot--anything else you haven't found yet. If you only plan to work on the boat without any thought of sailing her this season, toss the cushions and soft goods. If you'd like to be able to use the cabin, you may be able to salvage 'em enough to make using 'em bearable. Buy a bottle of Raritan K.O. and pump sprayer bottle...spray the cushions enough to penetrate 'em completely, then put 'em in the sun for a day. They'll still be ugly and dirty

...but at least they won't stink!Get back with me after you gone this far...we'll discuss what to do next. Few things are more satisfying than turning a floating "bag lady" back into an elegant lady.