What length of screws to use over 3/4″ plywood

The 45 degree decking is the primary sub-floor. It's a technique that was widely used in the past, but has subsequently been replaced with simply dropping sheets of plywood down.

In answer to your questions:

1) You can glue and screw to the sub-floor.

2) In this case, it doesn't matter. The sub-floor is carrying the load diagonally. However, if there were no sub-floor, then you would want to go perpendicular. See this discussion on the subject.

3) Always - always - always level as you go. Fix the level at the soonest possible opportunity or it can be amplified by an order of magnitude.

Well technically it is plywood, it's just not very good plywood. Having said that I've seen flooring guys use a product that looked very much like luan that was no more than an 1/8 of an inch thick to get the level they needed. This was in a hospital remodel so it was definitely up to code and it went under a commercial grade thermo-sealed floor so it should be good for just about any application unless your subfloor is really atrocious. Ask around at a dedicated flooring supply store and they should be able to point you in the right direction.