Ok, still not clear on exactly how you're trying it (never seen SDC pop up a message on its own asking you to register GC2), so try this if it's not already what you did:
1) Go to the Tools menu in SDC, and choose Register Products.
2) Pick Games on the left in the Register Products window, then find GalCiv2 in the Product pull-down menu. Enter your email address (same as forum account, again) and serial number, then click Register. Repeat for Dark Avatar (use the same serial).
If that still won't work, then there may be a problem with your serial and
[email protected] would need to sort that out, as I don't have access to do it. Unfortunately the office is closed for the holidays, so it'd be a couple of weeks until you'd get any response from them. If your AP reg is also suddenly having problems then that also points at some deeper issue support would need to srot out.
You can change your email just by logging in with your SDC account on the forum here (which you should already be), and going to My Account at the top, then to Stardock Account. Confirm your login then you can change all your profile info.
There's no way to entirely eliminate class 0 planets, but you could mod all races to have a ridiculous planet quality bonus so that every planet you can colonize is huge.
A jewel case is the clear plastic case that CDs come in.