1. The 109 has an AvHistory 4.0 flight model, so it should be pretty much right. It didn't feel better than it should be flying against it. If you're comparing its maneuverability to what I was getting out of the Spitfire, there's a few factors to consider. First, as a result of the dives, my airspeed was often significantly higher than my ideal maneuvering speed, and on the early Spits with fabric-covered ailerons, this is particularly evident in roll rate. At other points I was not pulling as hard as I could because I could feel that I was on the edge of a stall, and at least once I overdid it and snap-rolled. Last, I took some damage to my left aileron, and possibly elsewhere, that reduced my maneuverability.
2. Not sure, but I assume it's still in there somewhere!
3. The reticle is fine for any of them, but the X, Y, and Z coordinates will be different on each model. The AvHistory and JF Battle of Britain Spits (but not JF's later Spitfire package) are all based on the same model, so what works for one works for the other. Anything else and you'll have to make your own adjustments to position it correctly.