Question

Trade ports are in the 4th level of the imperial tree, refineries are at the 3rd level.  Both are near the top of the imperial tech page.

The names are "Orbital Processing" (for refineries) and "Off-world exports" (for Trade Ports). Both in the Nanotechnology area at the top of the empire tree (as Darvin3 said).

Thanks, that's just what I needed.

Another thing I couldn't figure out was the phase stabilizers.  I don't know how to send my ships through them.  If you could help it would be appreciated.

You don't need to do anything. Any two phase stabilizers automatically send your ships between them when you give movement orders. They basically create hidden phase lanes that your ships automatically use - you just need a phase stab on each end, or an Antorak's/starbase's ultimate to create a temporary one.

Only one thing to add to that. Sometimes the phase lanes just seem to take a bit to pick up on the fact that they should exist. Like, if you have two phase lanes, sometimes it'll take 2 minutes or so for the phase lane to "exist" like annatar said. 

Which generally happens if you build a phase stab on a freshly colonized planet, the game takes several minutes to register it. If a planet has been colonized for more than 10-15 minutes, any phase stab built on it should register pretty much immediately. This has been a bug/issue/whatever you want to call it for a long time now

Another question I have is when I try to get on to Ironclad online.  I try to create an account, but when I try to 'accept' it tells me that I have the wrong version of Ironclad online.  And another thing is that I still have version 1.0 and when I try to 'download updates' it says that it can't find the web page.  What is going on???

And by the way, thank you all for your responses.  It's greatly appreciated.

It means you need to patch.  Patching is now handled by impulse.  Download impulse (the "downloads" button at the top of this very page will link you to it) and it will automatically update you to the latest version, allowing you to log into ICO.

Thanks alot everyone.  I have another question, I'm going to be getting a new computer soon and I was wondering if I would run into any registration problems when I re-register 'Sins' on Impulse and Ironclad Online?  Thanks again.

Nope; I have Sins installed on two computers myself for LAN purposes and have no problems.

Here's a really dumb question, how do you know when you beat the game.  I killed all of the computers, structures, planets, and ships and nothing is happening.  I didn't however colonize all of the planets.  Does that make a difference?

You've won the game when all your opponents have surrendered or are defeated.  A player or ai is considered defeated when it no longer owns any planets.  Once you've won, you will be prompted to either quit or keep playing.  If you keep playing, you're basically in a never-ending sandbox.  I think this is what you did by accident after your opponent surrendered.