Mark,
Early Cobras including well into the HP289 conversion used a iron case T-10s the same size and hook ups as a Galaxie I believe because that is where early car owners hunt parts from (early Galaxies that is). It is the later Galaxie Ford top loader unit that drops right in the place of T10s in Cobras for guys putting in stroker engines with more power than a T-10 can safely handle.
Rick,
So far I have not found anything different than260 Fairlane production except heads, intake, distributor, connecting rods, and camshaft.
#1 Not all Cobras to get 260s got HP 260s. One original owner car came with and still has its bone stock Fairlane 2V engine for example. An author friend that has interviewed (long ago) one of the people at the Ford engine lab that built up engines to send to Shelby and his associates (not all early cars were finished in California) indicated that they built up as many HP260s as they had parts for but if needed used and sent whatever they had.
Blocks - so far all that I know about are production Fairlane suffix J castings. One car owner has the engine for his car stored. As far as he knows the short block has never been apart as HP260 was replaced with a HP289 full race engine purchased from Shelby circa 1965. I hope to get to visit him and dismantle that engine for pictures this summer.
Cylinder heads - I have not found any claimed to have been from a HP260 with screw in studs. I believe some engines got stock heads but some came with strange XE numbered castings. The XE heads I held in my hands last summer did not have screw in studs.
Rods - I have only found a couple of short blocks or pieces of them left so far. One set of rods look very much like HP289 rods expect they have XE numbers on them. The set I examined last fall were right beside the XE heads.
Distributors - so far the best I can tell some HP260s in Cobras received Fairlane units modified for higher rpm. The common new car pictures show no vacuum advance.
Oil pans- stock Fairlane 221/260 with a temperature sensor added to their sumps.
Camshafts - this is the biggest mystery part. Last fall I obtained the original MECHANICAL flat tappet camshaft from a late HP260 engine out of a Cobra. The original buyer removed the part decades ago but kept it. It is a Ford casting and has a unique Ford casting code. I have sent it off to be completely analyzed and profiled so that after all these decades I might know what specifications were used.
Intakes - lots of versions here
1) At least one car, iron 2V Ford Fairlane
2) Some cars, cast iron Ford XE non-production 4V
3) Some cars, cast iron preproduction SK 4V
4) Some cars cast aluminum 4V Holman-Moody 260 Rally intake. The casting is very clearly based on the Ford 260 iron 2V intakes feature wise and port/runner design/sizes.
5) Some cars same as above except most of Holman-Moody thunderbird logo milled off.
6) Hand full at most of cars with COBRA aluminum 4V made from the reworked Holman-Moody pattern.
(One Shelby advertisement published in 1963 claims that this intake was the "stock" intake for Cobras with Ford Fairlane 260 engine. This intake was a regular factory option for Cobras until the high rise designs showed up at the very end of 1964. There is also a TIGER lettered version that was a dealer option for Tigers until sometime early 1965 when a TIGER high rise intake became available.)
Note: Legend says that a Holley R-2668 4V carburetor was the mate to the intakes I have listed above as numbers 4, 5, and 6. I have found just two pictures taken in 1963 that show a Holley with one of these intakes and the Holley shown is a R-2599.