You and your vet are probably correct in thinking this is territorial... and as others have said, females will martk territory too. Things might be more intense right now because of the season change. Even "fixed" cats sometimes react hormonally to the spring breeding season (that's assuming you live in a area with warm/cold seasons...I forgot to check). My guys always get into more fights and "play" sex (everyone is fixed!) when the weather warms up. Providing separate spaces and reintroductions (as everyone is saying) may help. Once they settle in and are used to each other it usually gets better. You may want to make your bedroom off limits to the suspects. It is most likely your "nest" that is the most contested spot and if they can't compete for it, it might help....It will certainly help you get a better night's sleep.