Ray,
By now I would have assumed you would have gotten a set of 65 Mustang Assembly Manuals. All the answers are there, the service numbers are not as the item were from the factor, they are for what works, and there in lies the problem we all have - what service numbers are direct (almost exact I hope) replacements.
First, there is only one battery tray for 64-66 Mustangs. Second, there are two clamps, one for the standard battery - it's the large clamp, and one for the large battery - the small one. Third, there are two stud plate retainers, a long one for the small battery, a short one for the large battery (the nuts should be the same but "variations" appear after 50 years). Fifth, there are two batteries, a group 24, the small one, and a group 27, the large one. Do not be concerned with cranking amperages as there is one small battery, and one large battery being reproduced. The original different rates were for "cheap" and "expensive" batteries in the two different sizes. You may find that current reproduction batteries are of the gel type, and more expensive.
The numbers: (the service numbers "may" appear on NOS labels for these items)
Tray - C5ZB-10572 - Service - C5ZZ-10732-C
Clamp, large - C2DB-10718-B - Service - C2DZ-10718-A
Clamp, small - C5GB-10718-A - Service - C5DZ-10718-A
Bolt, long - 380582-S2 - Service (don't bother)
Bolt, short - 379924-S2 - Service (don't bother)
To be truthful, with the price and lifespan of current aftermarket replacement batteries, and their lack of the ends retaining protrusion for standard installation, I use the aftermarket bolt-in bottom bracket, 2 ea 67 style long J-hook bolts, a 67 style top bar and two wing nuts for daily use, plus a battery mat, all of which are easily removed for shows. The show battery is on a trickle charger. (I have more than one 65-66 Mustang.) One more thing in the list of stuff to be aware of, the batteries have a "F" after the number, 24F and 27F, which indicates where the positive terminal is located.
Jim