Well, safe to say we know the cause of the problem. You have boys and boy's can't aim! They say they can, they swear they do, but they don't! Case in point, some airports have started installing urinals with flies etched into the porcelain. Guys suddenly have something to aim at and the bathroom stays cleaner! Back to the point, I started having similar problems with stinky smells when my boys were potty trained. I kept buying new cleaning products, thinking that was the problem. Finally, I asked a friend to come and help me. She has 3 sons and loves to clean! She taught me a lesson on bathroom cleaning. First, she used bleach! Clorox Clean-up to be exact. I had been avoiding bleach because I was worried about the kids breathing it or touching it. She reminded me that bleach breaks down pretty fast and is not dangerous after a few hours, sooner if you rinse well! It really zaps the stink out of the ahem, residue, around the bathroom. Then she showed me that I was missing about 60% of the 'splash zone' and leaving a lot of unpleasantness there to be stinky. I really had no idea that my kids were missing as badly as they were! There was pee on the shower curtain! On the side of the vanity! On the wall behind the toilet! On the trash can! What were my kids doing in there?! I was spending all this time cleaning the seat and the base of the toilet, and in FRONT of the toilet, I had no idea they were peeing BEHIND the toilet! Gross! I mean, I washed the floor back there, but the WALL?!

Following her directions, I started focusing on the entire outside of the toilet. Up under the rim on the outside, where the bolts go through, down the back of the base, way up under where the base and the tank meet behind the seat, places I just never imagined would be that dirty! When I lived alone I never had to clean pee out from UNDER the toilet! I also extended my reach, hitting up the walls, vanity, trash can, toilet paper holder, etc. even if I didn't think they could possibly reach there!
I bought a new toilet seat. It comes off the bowl so I can get all around the hinge area really well. I pull it off, spray it down and let it sit in the tub and disinfect while I clean the rest of the toilet. Even better, it is 'slam proof!' it just closes slowly and quietly, both the seat and the lid!
I also tossed the other cleaners and started using bleach. After the initial scrubbing is done and the mats in the washer, I spray the whole bathroom with the bleachy cleaner, making sure to saturate the tile grout all around the toilet. Then I put on the fan, blockade the door and leave it to sit for half an hour or so. Then I rinse it all down really well and mop up the floor. Ahhh! It takes a little while for the bleach smell to dissipate but once it does, it just smells clean! No more lingering pee smell!
For the record, that Clorox Clean-up will also take toothpaste, lip gloss and red fingerpaint off the walls, door and floor! I don't even want to know how it got there in the first place, but it's gone now!

I recall seeing a cute little wall hanging once that read "If you sprinkle when you tinkle, please be neat and wipe the seat." And one that read "My aim is to keep this room clean. Your aim will help!" Cute yes, but not very effective for young boys. I think a better idea would be to take a permanent marker and write "If you can see this LIFT THE SEAT!!" on the toilet seat! Or, just teach them to sit when they pee!