"What would you suggest as a non- chlorine remedy to add to shower drain, and stuffing box area that drips and leads salt water to bilge? I used a 50/50 chlorine/water solution, but it sounds like that should be discouraged."
Glad to hear you have had success with the odors. It is a constant process. Unfortunately, the only way to keep odors down really is to clean with soap, rags, sponges, water. Even the soap should be washed off. The bilge will always be accumulating "stuff" - salt water, dead and live stuff, dirt, not to mention oil/diesel that isn't caught 100% by sorbs, etc. - even on a relatively clean boat. Check out the Peggy Hall book. It doesn't have anything earth shattering in there, and not a ton of scientific anything, and even a bit underwhelming, but what it does have is good and solid. At least it isn't very expensive.
But ditch the bleach from your cleaning kit. Like several have said before, it doesn't really take care of the fundamental problem. It will kill germs that might be hazardous if ingested or in a cut but the best way to deal with that is just soap and water (except minor treatments on occasion in your water tanks). If you clean your toilet on the outside or the inside with bleach containing products you will kill the germs OK but it will also get in the holding tank and in the bilge unless completely wiped off and kill the "good" germs.
As noted above nitrates may not be the best thing to discharge overboard. Not all products for this contain nitrates so you have to do your own research. The KO products are really for the holding tank which is pumped out to onshore facilities. Any minor amounts used in a spray is not a big deal IMHO but it does all add up. I personally try to limit anything that goes in the water that wouldn't normally be there. Please write to the City of Victoria, BC, Canada and please ask them to quit pumping 100% of this big city's untreated sewage out in to the Straits of Juan de Fuca. We sail by there pretty often.