Part of the following is based on an article which appeared in an issue of "Mustang Monthly" back in the early '90s detailing the history of Ford/Rotunda/Autolite/Motorcraft oil filters.
At the engine assembly plant, filters were installed which were devoid of markings other than a stamped part number on the end (top) and may have had a "Use Genuine FoMoCo Replacement Parts" graphic printed on the side (see the '64 Shop Manual in the Engine section for an example). Through '65 these "break in" filters were painted black, and this changed to Corporate Blue for '66 to match the block color.
The red Rotunda R-1A assembly is a replacement for the break-in filter which was marketed through Ford dealers as well as other retail outlets (much like the Motorcraft filters are marketed today). It made its appearance during the '61 model year: provided the dealer bought the Rotunda filters for their inventory versus going outside of the corporate chain (i.e. buying Fram, Autolite, Pur-O-Lator, Wix, etc.), this would be what would be installed on a car in order to maintain the car's warranty, especially as the car came in for service work. Prior to fall '61, the body of the filter with the two-stage crenelated "Rotunda" top was probably painted creme and red/brown to match then-used Rotunda/FoMoCo graphics (this can be seen in illustrations in the '60-'64 "Blue Bible"), and most certainly would have also seen use on cars like the Squarebirds and early Bulletbirds as dealers used up existing supplies and replaced them with the red R-1As (and I'm not even factoring in the original-design disposable filter used '58-'60 without the "Rotunda"-style top).
Production of the red R-1A continued through the spring-summer of '65, when Ford began to advertise in "Shop Tips" magazine (which was distributed to service stations, fleet repair shops, etc.) that they were having a close-out sale on this filter. Dealers were encouraged to buy the red-cased filters at a greater discount than normal, which probably resulted in a lot of dealerships having an abundance of red R-1As to use up through the coming '66 model year.
The gold "6000 Mile" design filter was rolled out during the summer of 1965 to coincide with the '66 model year introduction, and used the same "Rotunda"-style top. As noted before, the car was delivered from the factory with a break-in filter, which would be replaced during service/warranty work by dealers. The red-cased filters would have been available in quantity early in the '66 model year, but stocks would have diminished as time progressed and the gold-cased filters were bought to replenish inventory. Interestingly, Ford/Rotunda also offered "6000 Mile" motor oil in the same graphic scheme on quart oil cans (remember oil cans?).
During the summer of 1966, to coincide with the '67 model introduction, Ford began to switch branding of service parts like oil filters from Rotunda to Autolite. The first-generation Autolite FL-1 filter became available by the fall of 1966, had the same case design with "Rotunda"-style top, with a white body along with red and black graphics. The graphic design changed was updated during 1968 and the case design changed to the same style now used on Motorcraft FL-1As, with "Autolite" stamped in the end/top.
So, which filters are "correct" for each triennial? If based upon period when filters were in widespread use/production and when a car was built, the red R-1As would be correct for '61-'63 and '64-'65 as well as '66, and the gold for '66 as well. Or, it depends upon what day you dial in your time machine...
Alan H. Tast AIA
President, Vintage Thunderbird Club Int'l.
Author, "Thunderbird 1955-66"