I hate to say it but I have NONE of these problems, well sort of, there is one that you have that I had that is because of the way M2D locks down the files (luckily there is a program to do it for you). You can't install the themes to change the M2D interface as a cab. You need to use a program like M2DC (Manilla2D Customizer). It will give you a graphical interface to customize m2d to your hearts content.
You can find the program here:
http://forum.xda-developers.com/showthread.php?t=427392
Just leave the files as a zip or cab and you can browse to them and select them. It will take care of the rest. You can customize what buttons show at the bottom, their order etc. IT IS WONDERFUL and for me works great.
Unfortunately, I can't help ya with the rest.