One thing I noticed was that you said you clean his litterbox every other day. Usually, cats are fastidious creatures and, as such, like to have their litterboxes cleaned on a daily basis. I clean mine twice a day, sometimes more often, but then I have 7 cats. But you wouldn't flush your toilet every other day, so give that a whirl and see what happens. Of course, make sure it isn't something more serious. But I know that my Peeka (RIP) would test the waters, so to speak, by putting her paw in the box and if it didn't feel right to her, she wouldn't go in. Then I'd find her calling card somewhere in the house.

Blessings,
Mary