Starting with the plastic box...

1. The nut and washer, if you are correct, will fit the jack. The nut for the jack will ONLY fit the jack so it should be easy to figure out. The plastic cover is exactly what you thought.

2. Screws are probably for the pickup rings. They look too short to be for the pickups. The other thing is a pickguard bracket, mounted like in the pic. It's common if you add the pickguard on an archtop.

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3. Strap buttons, yes. The front one goes roughly where this fellow has his. Usually on or just behind the heel.

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4. Hard to see, but sounds right.

5 & 6 seem right.

Your dry fit looks reasonably good, so this many not be an issue, but really the most important thing before drilling holes is to make sure that the strings align well with the bridge--or in this case the tailpiece. Since this has a floating tailpiece, a mm one way or the other should not make too much difference.

With regard to the extra hole under where the tailpiece mounts, what I might be inclined to do is get a third screw that looks like the others for the tailpiece, and put the strap button in the hole drilled in the wood. The strap button often goes at the end of the tailpiece, but I don't think there is any law that says it must ;-)