[scr8pdo]

If you feel confident enough, I would remove the belt (lock it up first) and see if you can get them marks spot on ie turn it back a tooth, once you have done this and retensioned belt, turn over by hand twice and see if all lines up again, sometimes an engine can look a tooth out but when you go to put it back a tooth its miles out meaning it was right in the first place, have you checked the tensioner for play or and idler pulleys if there is any?

As I say if after you have moved it back a tooth and it all lines up better than before after turning it over by hand cranking twice, then i think you would have solved it!