A few comments...
The hose that's the most susceptible to odor permeation is any tank discharge hose that's connected to a fitting at the bottom of the tank...'cuz sewage will always rise in that hose to the level in the tank, standing in it. And while boat builders try to cut costs by using clear water hose for head intake and tank vent line, that's actually a BIG no-no. Only sanitation hose should be used throughout the system.
Stagnant sea water trapped in the head intake is a major source of TEMPORARY odor...odor that goes away as soon as the first flush flushes all the stagnant water out of the intake and pump. Teeing the intake line into the head sink drain line is an excellent solution, 'cuz it provides a means providing clean fresh water to rinse the sea water out of the WHOLE system before it can stagnate. Unfortunately just pouring fresh water into the bowl doesn't work very well...'cuz bowl contents aren't recirculated through the intake line, pump and channel in the rim of the bowl (thank goodness!)....whatever is in the bowl only goes out the bottom part of the pump and down the discharge line.
Ron said, "The first step is to clean out the existing bilge and I found that one of the best items is dishwasher detergent - it's low to no sudzing and cheap. Leave it in the bilge (to slosh about) while the boat is docked (for a week) and pump it out later."
Ooooh, Ron...don' do dat!! Dishwasher detergent is HIGHLY caustic..if you question that, just pour a little into your hand, wet it and see--or rather feel--what happens! It's very damaging to rubber in pumps, rubber wiring insulation etc in the bilge. But even if you use a detergent that is ok, you cannot end up with a clean bilge if all you do is dump something into it and then pump out the dirty water...any more than you'd end up with a clean kitchen sink if did nothing more than pour some Dawn into greasy dirty dishwater, swished it around a bit and then just pulled the plug. Ya gotta put some effort into it and flush ALL the dirty water out. This is where a power washer can really earn its keep...'cuz it can get into places you can't reach. I wouldn't be without one!
Roc...I dunno why you use fresh water to flush all the time...As Ron said, it's the last flush before the boat will sit that matters...flushing all the sea water out. It certainly doesn't make any difference in the holding tank tank whether the toilet is flushed with fresh water or salt...there's so much bacteria in the waste that what's in salt water isn't even noticed in the tank. So save your fresh water and just be sure to flush out the system with it before the boat sits.
And finally, in another discussion someone said they thought that sea water mineral buildup is salt precipitated by urine. Nope...that buildup is actually sea water calcium carbonate, which can build up in any anaerobic environment such as the inside of hoses...and that includes engine intake and exhaust hoses. And from what I saw in the photos posted, I'd strongly recommend checking those hoses. A really serious buildup can be dissolved with muriatic (sulfuric) acid without damage to anything the system. However, hoses need to be inspected often enough to prevent a really serious buildup like that in the photos...that's the worst I've EVER seen in the 20+ years I've spent solving sanitation and odor problems.