Sounds like you are referring to the early Shelby setup. If that's the case the standard Mustang V8 29/32" cylinders should work, that's what the 65-66 GT350's used. Ford part numbers C3OZ-2261-B and C3OZ-2262-B.
Some people believe the early GT350's used 15/16" cylinders since the 10x2.5" rear setup was sourced from the Fairlane wagon and that's what they had, but so far every 65-66 GT350 owner I've spoken with that still has the original rear cylinders have the 29/32" ones.
Dave