Go to the vets, there's a product called "Urine OFF!" which is in a black bottle - it removes all smells. Excellent stuff.
Secondly, don't use amonia-based products to clean up the urine, it will only encourage him to put his scent down.

As for meowing at the door, he's just learning that he's an inside cat. That will take some time, and he has a little friend, and will learn that he is with you and a good couple of meels a day from now on.