Pertronix ignitions have a reputation for being troublesome in both motorcycle and automotive applications that I'm aware of. You might save yourself some longterm trouble by using the original distributor with a pickup for either a factory HEI ignition or an MSD. Or, once you solve the length mystery using a factory SBC HEI distributor. I can't speak to the distributor shaft length problem as it's a new one on me.

1951 3800 1-ton
"Earning its keep from the get-go"
In the DITY Gallery
1962 261 (w/cam, Fenton headers, 2 carbs, MSD ign.), SM420 & Brown-Lipe 6231A 3spd aux. trans, stock axles & brakes. Owned since 1971.