I figured out how to set up the basic buttons like start, action palette and to move around via the in game options, however, I'd like to make L2 "CTRL" and R2 "END" so that i can quick change with my controller, how do I do this?

Well, I can't really one button all that (I don't use the second bumpers), but I use R1 for Ctrl and Triangle for End, so if I like to use the quick menu, I just do R1 + Triangle, which is just Ctrl + End.

You are familiar with this? Yeah, it would make sense for you to want a better pad configuration then.

You can try something like XPadder, but I don't really know how that works.