Very little was done to short block assemblies by Shelby American at the way through the 1967 Mustang Group II season.
1963 team Cobra short block assemblies were almost stock except for
oil pump pickup bracing that Ford developed in 1961, a shim behind the
oil pump internal relief spring, larger capacity
oil pans, better balancing than Ford’s assembly line, and safety wiring of some critical fasteners. Even with the upper end modifications of ported cylinder heads and 4-2V induction system the stock cam shafts Ford installed were used. XHP-260 engines had weird camshafts. HP260 engines had a cam shaft that was the parent of the HP289 stock cam shaft. The stock HP289 cam shaft was used and sold as a racing part for years.
By 1965 Ford’s Don Sullivan created a family of cam shafts for Shelby to use. The final version was sold by Ford for years as a race part. Engle made custom ground cam shafts for Shelby American in that time frame also. By 1965 Shelby American was fond of drilling, tapping, and plugging the steam holes in cylinder blocks. They were also fond of having the contractors doing cylinder head work weld up the “banana” steam holes in cylinder heads. The engines for 1965 MUSTANG GT350s had the press in core plugs at one end of the lifter oil galleries removed and sealed with threaded plugs. Crankshaft journals had oil grooves cut into them.
1965-1967 some of the teams C6FE-A racing cylinder heads got rings cut into their decks for metal combustion chamber sealing rings and some did not. Set five was so modified and we have that set in our red car currently.
1967 was the last year for 289s and the pistons Ford included in the Group II crate engines were stock HP289 pistons with valve reliefs enlarged for using C6FE-A cylinder head assemblies.
On the Ford front there were all kinds of prototype, experimental and limited manufacture small block engines. The aluminum 255 INDY push rod engine didn’t work out too well. One was very briefly tested in a Cobra before it had a failure. The Single Over Head Cam HP289 didn’t make it past testing (Rumor says that exhaust flow was the problem because Ford wanted to use stock HP289 cast iron exhaust manifolds. ). There were 1965 and 1966 versions of steel crankshafts and four bolt main cylinder blocks.
All that said, building a duplicate of a 1963-65 Shelby team race engine long block assembly is very easy, just start with a real nice assembly line HP289. Most of what was described above was reported with pictures in most of the automotive magazines in the USA and some abroad in period. The induction systems (many versions) are what the typical weekend warrior would have not been able to afford or maybe just rationalize. In 1963 the 4-2V Cobra induction kit had a suggested retail price of $1,230.70. There were some new cars one could buy in that price range. In period it was predominately extra wealthy owners that had “Webers” on their racing Cobra. The not so rich racers used everything from the stock 4V iron intakes to whatever came out each new season in the aftermarket. The original owner / racer of a new 1964 Cobra had a circa 1967 picture on the wall of his car with two holes in the bonnet and air cleaners poking out of those holes. He raced in SCCA with a very tall 2-4V cross ram induction system. Name a brand and style of “racing” intake for one or more carburetors sold between 1965 and let’s say 1972 and at one time or another and I probably saw one on a Cobra except for a Man-A-Fre® 4-2V.