You should continue using the same registration code that was initially provided to you. If you no longer have the email with your registration code and are registered on the PokerTracker website you can view your code directly on the site under My Account -> Registration Codes.
Please see the PokerTracker 3 - Free Trial page for details on how to take advantage of the free trial.
Yes. However, each virtual machine installation counts as one of your two usages per registration code regardless if they are on the same physical computer.
If you install PokerTracker on your computer then install it on a virtual machine on the same computer this would count as the maximum of two allowed usages per registration code.