reises58,
First off, welcome! Looks like you've got a good project to work on!
I see a lot from the images you've posted. Many of your questions about what is right (or wrong) can be seen on the CJ3B Page (link is the 3B image on top of this page). I'd start with the Tech section and look at, "Dating By Interior Details." Also read what's posted in the Paint section (will give you colors on nearly everything attached to your jeep) and then scroll down to find the "Tailgate Construction, " article under BODY. Then head over to "Owners Photos" and really scan through the 1964 section studying the images that show detail. I've spent hours looking at all the information posted and still haven't read everything (yeah, it keeps growing too!).
Based on what you've posted so far, I'd say the Previous Owner (PO), had a little fun with some of the items you pointed out. An aftermarket toolbox can be bought. An original used (take-off) tool box can be bought - complete with some degree of wear/tear (this will hold true on most components, incl seats and breather, depending on your pocket book and patience). The instrument panel will need a lot of work and I see (at least one) cut-out in your fire wall too.
Initially, I'd ask is it drivable? I can't see a radiator but what did the seller reveal to you? Are you wanting to drive right away or disassemble to rebuild?