1) Not possible. You'd have to replace the matrix system with a terrain system or tiled 3D plane objects.
The Matrix1 utilities plugin features a multi tiled 3D plane construction function which can be developed to behave like a hybrid of a matrix object and a terrain. If you really love using matrix objects, then you could consider using post rendering shaders to improve the look of the overal visual experience by compositing the camera view.
2) If the mouse leaves the window then use Position Mouse to return the mouse to its previous position in the window; if the window has focus. If it does not have focus, then leave the mouse position alone.
If there is no need to use the mouse cursor for clicking on items or user interface buttons; position the mouse cursor in the center of the window and hide the mouse cursor.
3) I can't help you there; but I would avoid using native 2D text commands; if you are using them; I would rather use text plugins made to improve on the native, or sprites, windows controls, and textured 3D objects with text, which perform far better and can be more consistent.
I have experienced something similar with print/text commands where some text flashes and gets displaced for some strange reason. I only use such commands for debugging. After using the tool for the past 5 years, I have found that drawing text onto textures for sprites or 3D objects is the best solution for performance and reliability.
Nice looking game by the way
