So it looks like the blocked vents were causing the holding tank to pressurise during flushing and forcing effluent into the macerator discharge line, which allowed seawater to siphon back into the holding tank. It also meant that sewage gases could not vent overboard and were finding their way out through any means (probably the fittings where the filters used to be) into the bilge area of the boat and, ultimately, our stateroom.
I was gearing to repeat what I've said so many times, that unless a tank is leaking, it's rarely if ever the source of odor INSIDE the boat because odor from the tank has only one place to go: out the vent. Then I read that there are TWO fittings in your all-but-blocked vent line, which is where air --and odor--from inside the tank was escaping.
Why in the world would anyone splice a piece of hose into a vent line instead of just replacing the vent line?????
You mentioned that the vent thru-hulls had rusted. All "vent" thru-hulls are actually designed for use on fuel tank tank vents, so they have spark arrestors and the smallest openings possible to keep sea water from contaminating the fuel supply. Boat builders use 'em on every vent because it's cheaper than using a different one for each application. That's ok for fuel and water, but not for waster because they cause more problems than the solve or prevent..and they make it difficult to keep the vent line clear. So if you want to avoid a repeat of the same problems, I strongly recommend that you do the following:
1. replace the vent line
2.replace the "vent" thru-hull with a plain ol' open "bulkhead" or "mushroom" thru-hull. That will allow you to stick a hose against it and backflush the vent every time you wash the boat. Accumulated waste from your overflowing the tank and any "critters" who've tried set up housekeeping in the vent line will be flushed into the tank.
3. Put a tank level indicator on the tank! There's no excuse to overflow the tank out the vent, and as you've already learned it causes big problems. These are the top rated systems: Scad Tank Monitors
(actually made by these people Profile Tank Monitors
and private label branded by Scad). The "Solo" is inexpensive and very easy to install...the sender goes on the outside of the tank.
Safety standards call for keeping the overboard discharge thru-hull closed except when actually in use. You're obviously keeping it open all the time 'cuz I'm sure you aren't opening it to dump the tank OR closing it afterward. You could relocate the thru-hull to make that easier...or, if the rest of your sanitation system plumbing is as jury-rigged as the tank vent line, keep on keepin' on till the day you see your spare deck shoes floating in the cabin.