Is it true that Canvas3D negates all the bonuses achieved from Fullscreenmode since it is heavyweight?
No.
Is there any way to disable the innate AWTEvent processing and implement your own on top of it? The way I see this, it would give a nice speed boost to customize the code work with the rendering engine and FPS update interval.
Just don't produce events. Then the event thread just sleeps. I've never heard that the event thread itself produced any noticable load.
What internat threads can be accessed by the program? It would help a lot if I could implement one of those internal threads to do the input monitoring
It already does. That's the event thread.
and perhaps the game physics(collision detection). This would leave the main game thread totally free of unneccescities.
Physics in the input processing thread? Normally physics runs as an integral part of the gameloop and does not count under 'unneccescities'.
Does anyone have any tips and tricks what to do to get the optimal performance by tweaking the innate processes without JNI?
Just use them, they are fine.