I can see how long-term stagnant water in pipes & toilets can cause a bad smell, but shouldn't you be able to just occasionally flush them or run the water through & that be enough to keep things fresh?
This is really terrible, but we had friends who smelled something awful in their new house, only to find out that the construction workers who built it had been using a large, 5 gallon paint bucket as a urinal. Apparently, when the dry wall went up, they enclosed it in the walls!
I wouldn't have believed their story except for the fact that when our house was being built we went to check the progress once & our master bedroom closet had a large styrofoam cup on a shelf filled with urine. Disgusting. They also filled our marble garden tub with food & trash which attracted ants. Even though we kept our bathroom spotless, we had ant problems around that tub for a good two years after moving in. My point is that some builders don't seem to care enough about the people who end up living in the houses they build!
If I had it to do over, I would have thrown a fit & had the builder come out & find the source of the smell before our warranty ran out. If we ever build again, I'll be at the site every day checking up on them. I'll also be sure to inspect before the walls go up.
In another home we had a bad smell like something dead & I never found the source. I was convinced it was a dead mouse behind the walls. The smell was terrible, but eventually it went away on it's own, so if you don't discover the exact source of your problem, don't despair, it won't last forever.
In the meantime, I used essential oils to purify the air & improve the smell of our kitchen.