Can a 'hotkey' be setup to focus a particular browser window? If so, how to create it AND will it work for the major browser (IE, Netscape, Firefox, Opera, et al)?
Only windows you've named and created via Javascript can be accessed via Javascript and then you can trap keystrokes or whatever else you want. If you want something more powerful, you'd have to code an extension to the browser, but alt-tab switching (and the good-old clicking) usually suffices for most users.
The browser windows I'm referring to were created via JavaScript. How would I add the necessary keystrokes that are not overriding the browser defaults and those same keystrokes work the same in all major browsers for PC and Mac OS?
Well, you'd have to choose a keystroke not used anywhere else (I don't know Macs) and which had keys on both keyboards. Then use a JS keystroke catcher to process access the window. Tips on manipulating windows can be found here: http://www.quirksmode.org/js/croswin.html