How to install from a back-up

There HAS to be an easy anwser to this, I'm just an idiot.
The deal.
I want everything (Applications, and settings, etc) on my "Old" computer transfered to my "New" one.
We moved. Overseas. In doing so we bought a "new" iMac (left the old one stateside). I have an external HD that we ran Time machine on from the "Old" iMac.
I have already used Migration Assistant (2.5 hours of migrating, thanks USB 2.0 ). We thought it would work, but though the applications are present, we have to re-enter serial numbers, and settings didn't come through (things like presets in Aperature are not present).
We had a HD crash on our "Old" iMac, and after getting fixed, we did some kid of reboot from the Time Machine Back-Up, and everything was honky-dory. Is it because it was the same machine?
A side note, when we bought our "New" iMac, we had them install more RAM. When we got home and first turned the machine on, it just booted up. We didn't get that usual cool video of "Welcome! Bienvenue!...You are awesome for buying a Mac!" video that plays at the very beginning when you boot a new product. Do we need to somehow do a "super-reboot"?
I'm no expert, but I can usually figure something like this out. But it ain't coming together today! Any help is greatly appreciated
Thanks ahead of time.
Your's
Grinding Rage Rebooter (Grr)

Start here: https://discussions.apple.com/docs/DOC-4055

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