I've pasted the process from the email you didn't receive, it all went very smooth for me. I think if you have the serial you should be good to go. Everything went thru stardock central...

HTH -

Downloading Galactic Civilizations II:

1. Install Stardock Central and configure it with your Stardock.net
account information when prompted. If you have a firewall, proxy
server, or the like, please set it to allow Stardock Central access
to the Internet.

2. If your account information is all set, Stardock Central should
see your registration and allow you to download the base game
and the modules (click the + next to the game listing in the
Games section).

3. If your account information is not picked up, you can use
Tools / Register Products to enter in your serial number directly
(copy and paste from this email). Press the Update Now button
to validate that with the server.

4. If you are having difficulties, please visit
https://www.galciv2.com/forums.aspx?ForumID=162&AID=100878&p=1
and see the information in the first post about how to help us
troubleshoot.

I still can't believe that I am one of the few people who still see's the benefit of paying hard-cash

Cash is so last century. Pay online, direct download is the way to go(most of the time I guess). Stardock will even ship you a cd copy for free(at least they didnt charge me shipping for mine)

Anyways to the guy who hasnt gotten his activiation code yet, isnt there an option in Stardock to have them resend your serial numbers(yep just looked, go to Tool--> Look up serial). Just put in your email address(I believe you might have to make sure your stardock email and your paypal email are the same), and you should get your serial sent to you again. I think that is all automated so assuming the paypal payment went through fine you should get that email within a few minutes.