Agree that generally you've got to get down to clean metal in order to do a proper job of keeping corrosion away. Rust converters are helpful but only after you've done the bulk of the work of getting the rust off the metal. We have several items constructed of mild steel on the boat--the large windlass case and various parts of the steering system come to mind. I sanded all of them, treated them with a rust converter, rinse, and then rust converter primer before painting. Lot of work. Your deck is bigger and will be even more work but well worth doing.
Several of the things you mention are the sort that you'd get excellent advice from a reputable surveyor. If you did not have your boat fully surveyed when purchased, now is the time to figure it all out. Our boat is wood, not steel--so can't help there, but we hired an excellent surveyor familiar with wooden boats who worked with us from the get-go to identify and stay on top of all things which require maintenance, repair, replacement. As we went through a major rebuild we continued to call him in periodically. It was well worth the money.
A surveyor can point you in the direction of a boat yard or craftsperson to do things you don't want to take on yourself. If you're not an excellent welder already and quite familiar with the needs of steel hulls I'd think you'd be very happy to have a good steel-boat surveyor in to take a look.
Regarding toilet--if you have direct discharge w/o a holding tank, I can see the problem you might wish to get rid of. However, installation of a holding tank system seems most logical. We have two toilets--one is a composting head (Natures Head and Air Head are the two USA brands) for use most times and the other is an offshore only use direct discharge w/o holding tank (legal to have in USA IF installed before 1978 or so AND locked down so it cannot be used unless out to sea). If you don't have room for two, then the holding tank is likely the way to go. If you don't have room for a holding tank, then a composting toilet is worth consideration. With it, you will have to remove a couple gallon liquids holding tank and take it to a marina toilet every day or two but you'll only have to deal with the compost (solid waste) part every month or even less frequently depending upon how much you have access to shore side facilities so you don't have to use the toilet.
Best of luck in figuring out the right thru hulls to use--I prefer bronze but have a wood boat. Dunno how you deal with the dissimilar metals on a steel boat. A good surveyor can help you on this, though.