The 3259 is a derivative of (IIRC) the 2919 ( Dan will correct me) designed for a low riser 427. Dan and I have both seen these carbs in prototype form where the original list number was XXXXXXd out and 3259 was hand etched onto them. The major change was the float bowls ( obviously) The -1 revision was a change to the primary metering block.
Use whatever you want or like best. I do. I just don't "push" what "I" do onto others.
The base design was the R-2668A (Ford C3AE-9510-B) 427 4V carburetor in its 1964 configuration. Delete the square shaped fuel bowl assemblies, create a new version of the "center inlet" bowl assemblies used in the R-2919A 427 4V by changing to 0.110 inch inlet valve seats and DuPont® Viton® rubber resin tipped inlet needles, change the left side fittings to install a transfer tube, and add the transfer tube and presto a R-3259 prototype.
The drawings released December 2, 1964 detailed all the parts including all calibrated orifices for the production R-3259A. The R-3259A was only made in two runs in December 1964. In January the R-3259AAS model went into production; Ford C5AZ-9510-A or Shelby S1MS-9510-A. During the 1966 model year the R-3259-1A (Ford and Shelby S2MS-9510-A) was released and before June 1966 the final production version R-3259-1AAS was put into production.
Holley indicates that R-3259 and R-3259A models were rated at 700 c.f.m.. All the others were described as either 713 c.f.m. or 715 c.f.m. depending on who published what when.
Each new suffix denoted a change in functionality. Most changes R-3259 to R-3259-1AAS were made to improve the air fuel mixture curves and make wide open throttle acceleration of the car quicker. The biggest single functional change was the R-3259-1A that introduced a new calibration for when secondaries started opening and how quickly they opened once opening started. The last change came during the R-3259-1AAS period when a new heavy duty main body went into production circa January 1967.
After all these decades of time many of the family of carburetors have had parts and features mixed around, especially by commercial rebuilders or people making up carburetors by finding one part at a time. It might take an hour to make a list of the common things people have done / failed to do which make their performance decline and or create driving problems.
This family of carburetors had a long development history, years. As designed they work very well puttering along at low rpm through a neighborhood in fourth gear or screaming down a straight at 8,000 or more rpm over and over. Some people make unwise changes that make for miserable driving. Other than float settings, the only changes I have ever found worth the time, and I tried all kinds of going the wrong way “improvements”, was changing main fuel jets and or power valve calibration to suit a specific engine build and or altitude. With no racing in mind I leave the power valve channels alone for high altitude as being rich during a wide open throttle sprint at 5,400 feet is better than being any lean at 1,000 feet and less.
The last Ford 'assembly line' variant that I am aware of was the R-3259-1AAS model with some customization of fittings and throttle lever for the GT40 MKIII application.