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It's a much easier task to observe and understand the design if you use Single Player Commands to get noclip/fly capabilities.

I'll take a look at your vault when I have time over the weekend.
I assume you're talking about the portal outside the vault in the overworld? It doesn't matter when you ignite that portal, so long as you ignite it before you try to enter it. =p
The only reason I leave it unlit is as a countermeasure against/indication of an edge-case intrusion scenario.

Hi Krackor, how are you doing?
I was wondering if you could please take a look at my vault...
And I have a question... with your design, I need to ignite the first portal before or after I input the code?
Thanks!