Ed,
From what I've read so far you are geared up for a full blown, high end restoration. To begin with, if you do not already have one, a good degital camera is worth its weight in gold. My suggestion is you begin by photographing and logging all of the items already disassembled from the car. The most important of which are detailed pics of any and all ID #'s, stampings, etc. Then I would move to the items still attached to the car. Begin here by photographing them in place and then once disassembled or removed continue with detailed ID pics here as well. As for tags, labels, chalk marks, paint marks, etc. absolutely... take pics of where these are located, and agian take close up pics of all important information that will aid in researching each of these. Once you have this information logged into your PC, you can always reference it as the need arises. Most importantly, you will have this information at you finger tips to use here to gain important information.
Good luck