Hey Matthew;
Just so you know, I'm not blowing off your PM, it's just that I waiting to find the time to get answers for you. I did mine almost 3 years ago and I simply don't remember where anything hooked up to. I'd basically have to tear apart my install to try to get you answers. I don't mind doing that, I just have a lot on my plate right now.
I know that I used a wiring diagram on the Commando site that I got access to after the purchase and it was reasonable. I think Bob ended up creating a better one after the group-purchase sweep. He's pretty well known for his write-ups.
Location wise - lemme say this... a lot of it will be determined by where you can fit the box given the length of the stock harness. You'll have more options if you extend the harness.
The key thing to remember here is that if someone wants your truck, they're gonna get it. And they're rank amateurs if they're still in the truck looking for the box if they've tripped the alarm, ya' know? Of course, that won't stop them from being stoopid, but...
Oh... Kudos for soldering! I can't tell you how many times I've seen crimp connectors be the cause of trouble - much like your twisted wire mess. yuk.