Thanks for the feedback guys.
What's odd about this is that I go on vacation once a year for the last 4 years and this is the first time this has happened. If it was a regular occurrence every time I left I wouldn't be as worried. I remembered reading that cats will go in unusual places to tell you that something is wrong so I called the vet clinic to ask about possible causes and they mentioned that I can bring him in for a urine sample to make sure nothing is wrong if it happens again. I'm working from for a few days and the weekend to help him get used to having me around as I think that should cure the problem.
As for scolding him, I learned long time ago that's not possible with this cat. He just licks your finger if you wag it at him calling him a bad kitty
He has been a tad more frantic with the meowing lately so I've been carrying him around more often which seems to calm him down.
As for the litter boxes, I've had them in the basement for 4 months and now and he's used them properly without any accidents and he had no problem going down 2 floors to use them in the middle of the night so I don't think he just got tired of going down so far all of a sudden.