As Winston stated - a vet visit is in order. The increase in yowling, the peeing outside the box are both indications that something is wrong. Remember he is part Siamese. They yap a lot all the time. But if it's increased he's trying to tell you in the only way he can. The kitty is not necessarily doing this to wake you up. He is trying to tell you something is off. How are his toilet habits normally? Have you noticed any colour in the litter? Like pink tinged to indicate blood in his urine.
I had just posted this in the other thread you responded to this morning. It has lots of good suggestions to help with scratching.
http://www.catscratching.com/
Also - some tips to help with the yowling.....
http://www.pets.ca/pettips/tips-43.htm
http://www.best-cat-art.com/crying-cat.html