JT, yes there is a difference. The HO engines used what are called "long branch" manifolds. They are, for the lack of a better description, a cast iron header. Quite good, actually.
Ram Air restorations in Texas makes reproductions of the long branches, in both stock form, and a 3" outlet. They can be had through all the normal Pontiac outlets (Ames Performance, Performance Years, Indian Adventures, etc.).
The large "single" air cleaners were used on all the big (non-GTO) cars. They aren't being repro'd, but there are still some on the market. I have a couple. One '63 and one '64.
You might want to look into Jim Hand's new book "How to Build Max-performance Pontiac V8s". There is a very good discussion on the manifold and air cleaner arrangements used by the factory, as well as the more modern approach to building the Injun engine. The book is available through most book companies, both online and at the stores. If you can't find it, e-mail me (
[email protected]), as I have a few. $18.95 plus shipping.