You can see illustrations of the domed 1/8" pipe plugs in primary metering blocks in any of the 427 Ford Holley 2-4V Technical Service Bulletins. I have never found a Ford hardware number for the brass pipe plug, steel pipe plug, or the 1964?-1967 straight thread plug. The 1969 service parts table has "PLUG (SPARK HOLE) - 1/8" HEX. SOCKET HEAD 87708-S(P14) listed as a service part. I have seen the hex head pipe plug in some R-3255/R-3255-1 service carburetors. Ford-Holley units R-2652, R-2652-1, R-2668, R-2804, R-2805, R-2919, R-3259, R-3259-1, R-3300, R-3301, R-3410, and R-3411 Ford Holley all used domed (rounded head) pipe plugs and probably more. Early plugs were brass. Some time during 1964 plated steel followed the brass part.
Holley parts wise:
Holley brass plug = ?
Holley plated steel plug = 7R-5
The manual choke bodies are different castings than ones for automatic transmissions. As unique assemblies from the casting onward they didn't need to be modified, they were just manufactured for HP289 applications with manual chokes.
All the 1963-64 Ford 4100As I looked up only had the 358165-S(II-65) 1/8" pipe connector listed (1/8" external thread pipe on one end for the carburetor, a hard vacuum line fitting connected to the other end.)
Lots of details for C3AF-S (HP390 and HP260), C3OF-AB, most C3OF-AJs, and all 1964-67 versions of Ford 4100A HP289 carburetors are hard to extremely hard to find.