Hey, at least the Finder has keyboard shortcuts. Do they even exist in Explorer yet? But you should probably be using PathFinder instead of Finder anyway (where everything is reconfigurable).

You're best off re-configuring shortcuts for the specific functions you want instead of trying to remap ctrl and command. Unless of course you simply wanted to move the functionality of the command key permanently to the ctrl key. In other words reposition the command key. And it sounds like that app will do that for you.

As far as reconfiguring specific shortcuts, you should use Keyboard Prefs for apps that don't already have the functionality built-in. You type the name of a menu item exactly as it appears in the app's menu and then the shortcut you'd like to use for it. You will easily be able to change the next tab command, but you will probably have a hard time changing word selection shortcuts.