Before doing ANYthing....
I suggest you spend some time reading the discussions in the Head Mistress forum. You'll find instructions for testing hoses to find out whether they're odor permeated...a simple permanent--and very inexpensive!--cure for sea water intake odor....and how to know if that IS the source of your odor...or is it the shower sump? Bilge? Wet dirty bilges and sumps are primordial swamps that can make a whole boat smell like a swamp or even a sewer.
You might also check out the link in my signature...you'll find the info there very useful too.
You say you need to replace the toilet...what makes you think so? If you actually do, you shouldn't have to pay the yard to do it...That's such a simple job that anyone who hasn't got at least that much mechanical ability shouldn't own a canoe, much less a 37' sailboat!
Replace hoses only if they stink or have gotten so old that they're hard and brittle. If you do have to replace any, replace ALL of 'em, not just one section.
Find your holding tank! And while you're looking for it, find every thru-hull on the boat...and check all the hose connections and seacocks to make sure that everything is tight and dry. 'Cuz when your deck shoes start floating about in the cabin is NOT the time to START looking for thru-hulls! :naughty:
And then come back with all the new questions you're bound to have...we'll be glad to help you answer 'em!