1. Generally the plane will fly as fast as the cruise speed listed in the aircraft.cfg file, as long as the plane's flight dynamics allow that (which is not always true). The speed listed in the flight plan is used for the sector calculations (see below).
FS AI is broken into "sectors". The plane's flight is broken into those sectors when the flight plan is compiled into a BGL file. That way FS only has to worry about the AI aircraft in the sector your plane is located. Unless you follow the aircraft along its path all the way, the time when it enters your sector is based on the location of that sector and the speed in the flight plan's aircraft.txt file for that aircraft.
2. I assume that when a flight is broken down for each sector perhaps the calculations result in varying airspeeds, etc. within each different sector? Also note that the planes airspeed will be different if climbing or descending.
3. I have found that the flight altitude in the flight plan will be used if the plane can climb to that level before ATC needs to bring it down, the plane's flight dynamics allow it, and the terrain is not higher than that.
4. I don't know if that data is available in any one place either. Generally, I use FL100 for unpressurized aircraft, FL230 for propeller airliners, and FL350 on up to FL410 for jet airliners.
The distances in FS is from airport to airport. Typically the distances on these web sites can be between the center of each city, the locations of city hall, or some other point. Thus they will vary.