Finished the job yesterday. Thought I finished on Sunday, but it turned out the Y valve was dripping, as well as one of the plastic hose fittings that screws into the "overboard" thru-hull. I replaced the old Jabsco Y-valve with a new Jabsco Y-valve. I know they get something of a bad rap in the threads I've seen, but seeing as I had already cut and run the hoses to fit one, I replaced like with like. Pretty easy job to replace, too - compared to the others. As for the plastic fittings, I pulled them from the thru-hulls themselves and re-taped the threads with teflon tape. Seems to be holding for now....
The new PHII pump pulls water into the head and pushes it out with gusto. I don't regret replacing entirely instead of just rebuilding.
I ended up using Trident 102 hose for the whole system, except for the raw water intake and sink drain. That was some sort of basic Max-flex cheaper hose, but I'm less concerned because those don't hold "troubled waters." Chances are, if/when some aspect of the system fails in the future, it won't be the hoses permeating.
Note: I went with 25 feet of 102 hose and that was just barely enough with maybe 2-3 feet of wastage. I used 2 feet of 1" Maxflex for the sink and maybe 2-2.5ft of 3/4" maxflex for raw water intake. I also used 6-7 feet of 1/2" clear water hose for the air vent to the holding tank.
Everything is much cleaner - there's still sort of a dank smell if the head door has been closed for a while, but I think that might be the residual dampness and old grossness under the sink cabinet. I cleaned that out a lot with bleach and paper towels, but it might require some additional attention. I'm also going to try putting a small passive dehumidifier down there to see if drying the whole area out helps -- who knows how long that Y-valve and other fittings were slowly drip drip dripping down there.
I had a mild heart attack last night when my brain convinced me I had plumbed the deck fitting to the top of the holding tank instead of the bottom. After pulling the whole v-berth apart again, and triple-checking, I did it right the first time.
All in all, it feels really good to have completed my first "big" project on the boat - one I have plenty of bumps and bruises to show for. It also has given me some confidence that no matter how screwed up a job gets in the moment, everything on the boat is ultimately a physical object that can be repaired, rehabilitated, or replaced. Thanks all for the advice/etc.