I'm sorry S., I know this is just frustrating but it made me chuckle. Mine peed across the bathroom wall above the toilet and across the tub one day just to see how far he could "make it go". Sometimes I think that little boys are just fascinated with where/how they pee.
Okay, being serious now - does your vent unscrew and come off? If so, wipe it out and do use Erica's baking soda suggestion to eliminate any odor. I take it you have told your son that he needs to be extra quiet during the day since Daddy is sleeping? He may be afraid to make any noise, hence his "relapse". To help Dad sleep you may want to invest in a white noise machine, blackout curtains, and earplugs for Dad so that he will not be bothered by small household noises. Also, weather permitting, spend more time outdoors with your children - though maybe not playing Red Rover under the bedroom window. Depending on the layout of your home, try and move the childrens' activities to the other side of the house, or move the sleeping Dad to the other side of the house. :)
Try and make it fun for the children - Daddy's gone topsy turvy - cook breakfast for supper once Dad is awake, and keep explaining to your children that although Dad's schedule has changed their schedule will remain the same. Make sure Dad has some time before he goes to work to interact with them - if he can, maybe he can read the bedtime story and tuck them in, then assure them that he will be home for "their" breakfast.
Ultimately, your children where adjust. Many parents work crazy hours and kids are resilient.
Good Luck.