I realize that if you are using all of the expnaions you reduce the investigator number by two and add one to the number of gates that can be open before the ancient one wakes up. But, this does not apply to the final battle. But what about for deciding if you draw one or two monsters when a gate opens? I played a five player games last night, which would be reduced to three players. Should we have been drawing two monsters when a gate opens or just one?

Just 1, but I think you'll find some of your investigators will be bored.

Depite the fact that, according to the rules, you'd only have one monster per gate, I'd play it two (and plan to for my 6/4) player games) Just because otherwise you're not going to have a dense enough monster population to threaten anybody. Five-Six investigators will obliterate one monster per gate, no matter how spread out the monsters are.