If the toilet uses sea water and the odor is pretty much confined to the head, is only there after the boat has been sitting and goes away once the toilet has been flushed, it's most likely sea water left and stagnate in the head intake. There's a simple inexpensive cure: tee the head intake into the head sink drain to provide a safe source of fresh water to rinse the sea water out of the whole system before the boat will sit. You'll find details in the discussions of "head intake odor" in the Head Mistress forum.
It can also be odor from the tank escaping into the head through a worn out joker valve. Joker valves should be replaced annually, especially in manual toilets.
If the odor is pervasive throughout the boat, the most common culprit is permeated sanitation hoses. You didn't really replace the toilet AND the tank but not the hoses? I can't imagine anyone doing that...but even some new hoses can permeate very quickly. Do the "hot wet rag" test on each one to test for permeation. The ONLY cure: new hoses. This time go with Trident 101 or 102 (identical except for color)
Trident Marine: Sanitation Hose It' costs a bit more, but is a double walled rubber hose that's been on the market for nearly 20 years without a single reported odor permeation failure...something that cannot be said about ANY other hose, not even SeaLand's highly touted "OdorSafe."
Or, whether you replaced the hoses or not, if you had spills when you replaced the tank and toilet, you could have residual odor. The solution to that to spray the affected areas with a product called "PureAyre"
PureAyre ...you'll also find information about how to use it in the Head Mistress forum.
And finally (Steve, are you listening?) ...If you just blindly jump to the conclusion that it IS the hoses, you could be wasting good money while failing to solve the problem....'cuz I get calls all the time from people who've replaced their whole sanitation system INCLUDING hoses, trying to get rid of what they thought was "head" odor...when all they really needed to do was clean their sumps and bilges--really CLEAN 'em this time, and flush ALL the dirty water out, instead of just dumping in some more "miracle" cleaner and/or bleach and calling it done. A wet dirty bilge or sump is a real "primordial soup" that, especially in hot weather, can make a whole boat smell like a swamp or even a sewer. Same is true of sumps. Cleaning 'em and KEEPING 'em clean will go a long way in elimnating boat odors.
Hunters are also notorious for a "grid" below the sole that traps water that also turns into a "primordial soup," especially if the fridge or ice box or AC condensate drains into the bilge instead of into a sump. That can be harder to find and eliminate, and may even require installing at least one new hatch in the sole (not hard or expensive to do and definitely worth doing!) to provide access to keep that area clean.
That should help you locate the source and point you in the right direction to eliminate the odor. I suggest you spend some time in the Head Mistress forum...lotta good info there...and you might also check out the link in my signature.
Please help head mistress!
So why am reading this in the Big Boats forum and not the Head Mistress forum???