Great! You have the right attitude, unlike many who start right in dismantling with good but misguided intentions.
1 - Remove the other water pump also. Good to start with known good pumps, so as to not revisit old problems that took it off the road. Try here for rebuilt with improved impellers: (You'll hear Skip's name here often.)
Skip Haney
www.fordcollector.com
Remanufactured coils and high volume modified water pumps for flatheads
Probably the best thing to do I know
2- Stay far away from electronic distributors. The distributor you have in hand is as good as it gets. Send it and the coil it has to Skip for a rebuild better than anything new and shiny.
What about an electronic conversion for the existing distributor?
3 - 6 v is all anyone needs. Changing to 12v is only a dirty band aid on oxidized wounds.
12 volt seemed like a good idea, modern, and maybe easier at times. I may look at a rewire so there are thoughts of converting it at that time.
4 - You haven't asked yet, but send the radiator out to be flushed and flow tested. Flush the block well before you install the pumps. Be sure to use a rust inhibitor in the distilled water you'll want to use in the system.
The radiator may have come from the engine donor car. Someone worked over the hood to provide clearence for the radiator so if it goes to the radiator shop I may have them shorten it also. What is this rust inhibitor? Are you talking about an antifreeze?
You're gonna want the EFV8CA book entitled 1938-39 Ford Book.
You'd do well to join the club, and maybe even a Regional Group as well!
https://www.earlyfordv8.org/early-ford-store.cfm
Is there information in there that is not availabe on-line?
And a reprint (or CD) of the Ford Service Bulletins.
http://cgfordparts.com/ufolder/fordpart.php?number=CD-38-48-SB
More questions?