I reviewed all the code changes you made.
Regarding the Manifest file, I have considered this in the past and decided against it. I do not want to require Admin privileges. I have been slowly redesigning how permissions are requested to remove unnecessary Admin access. The only thing in the CP that should require Admin access is installing/uninstalling services. It is not quite there yet but 3.2.1 should be close now. This allows people that are not able to use Admin due to environment/system restrictions to still use the Control Panel. If you want to enable Admin at each launch, you can configure your shortcut to always start with Admin. I do not want to remove the choice from the user.
For your second point, I see why you did it but it does not fully work. If you use the main interface, the Tomcat button will not become reactivated.
For your third point, I looked at the code and I do not know what you mean by this. I noticed you shrunk the overall main interface to use less screen space, made it always start in the middle of the screen, removed resizing, tweaked some font sizes, tweaked some character sets, and a few other things. The window maximize button still maximizes the whole form.
I think I would merge the size changes and interface tweaks. The button deactivation would need more work before merging those changes to work with all buttons. As stated, I do not want to require Admin at this point so I will also hold off on the manifest and leave the Admin choice to the end user.
Thanks for the feedback and work.