Epic, broski! 
MyPaint first starts working normally. I can use mouse and pen together. After using the pen for a while, only the middle button of the mouse works, but the right and left clicks do not respond. I cannot reach the main menu with the keyboard either…The same problem was with Alpha 2.0.
Do you mean by pressing the “context menu” button on your keyboard, or by pressing alt, because support for standard alt+mnemonic menu access have never been supported in MyPaint (due to arguably wonky keyboard input handling).
Need more details here. When you say “together”, I assume you don’t mean “at the same time”, because that is not supported and can even cause crashes (due to some buffering issue, I’m not familiar with the details of the input handling, you have to try quite hard to crash it).
This sounds like something to report on the issue tracker. Provide full information about your system, input devices, etc. Hopefully it’s something we can fix on our end, but there are no guarantees.
