Interesting questions, responses in bold...
May we get that train back on tracks?
What creates good tone?
- The old dry wood that vintage instruments have?
All wood used in instrument construction is dried. The wood in vintage instruments was relatively new when the classic recordings they're known for were made.
- The fact that the instrument has been played for a long time?
Instruments with little playing time also have good tone.
-Hand-wound vintage pickups and the effect of time on them?
Available today in scatter wound and "aged" pickups (with weaker magnets). My favorite aged pickup is the SD Antiquity and I prefer them to the vintage pickups I have.
- The quality of the manufacturing/workmanship?
Workmanship today in many cases is better than on many vintage instruments particularly those from the 70's.
- The quality and variety of wood used?
Same as used in the mass production of instruments today
- The strings?
Other than the player, the strings are the generators of tone.
- The worn out feel of an old neck?
I see that more as a influence on the player rather than directly on the tone.
- Can a relic match vintage?
Tone wise, yes.
- Can franken instruments sound as good as instruments which have been whole for 40 years?
Yes, as long as the "franken" is assembled properly (I've worked on more than a few that weren't) . It's simply chance which parts are selected on the production line when building an instrument.
- Is it the combination of several factors listed above?
Definitely
- Could tone be a random thing?
It definitely is. The number of variables and their permutations pretty much guarantee it, especially the variables concerning the material comprising the primary structural components, that is, the wood.
- Is it all in the head of the musician playing the instrument?
Depends on the musician.

