I would look for a Carter WCFB for a Ford/Lincoln/Merc and keep the original intake manifold. I have such a setup with the choke mechanism attached to the manifold. Yours should look similar.
You can buy a fresh 63 distributor from Autozone, but save the old Load-o-matic dual diaphragm or sell it on eBay.
I've heard that you can make the old Ford-o-matic transmission into a 3 speed auto, but I'd recommend conversion to a FMX. The conversion uses the stock bellhousing. Another option is buying the bellhousing to convert it to an AOD or similar modern 4 speed automatic. Worth considering, but get the brakes upgraded when you do
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The 6 volt system will work fine if you maintain it. They converted to 12 volt for a good reason, but the 6 volt worked for years and it can work for you. Use 0 gauge battery cables, not wimpy 4 gauge cables as found on 12 volt cars. Make good grounds all around. Remember that the coil will have the + terminal going to the distributor, not to the ignition switch. I've seen 8 volt (four cell) batteries used in 6 volt systems.
Nice car.
Best regards,
Paul Menten
Meridian, Idaho