The schema of buffer A is C. The schema of buffer B is D.
Each of the above statements associates one buffer to one schema. In all probability, buffer A lives within schema C, and buffer B lives in schema D. Other interpretations of "of" may be available, depending on context.
Of your examples, only the third makes sense. There are two schemas (or schemata) and two buffers. In referenced order, each schema is associated with each buffer. The meaning of "in referenced order" is encapsulated by the word "respectively".
The buffers A and B are (in that order / respectively) associated with the schemata C and D.
Two buffers in the subject. Two schemata in the object of the preposition in the predicate. Ordering constraints apply. Subjects and objects are plural. Pairings are unique and singular.
Your first sentence makes no sense. It presents a single buffer named "A and B". It indicates a single schema called "C and D". There is nothing that makes the idea of "in that order" make sense. This is a one-to-one relationship without alternatives, without ordering, without any potential ambiguity.
Your second sentence makes no sense. It presents a single buffer named "A and B". In order, that one buffer has two residences. How can the order of one (and therefore an unordered) buffer match the order of two residences?
Your third sentence makes perfect sense. There are two buffers, one called "A" and another called "B". There are two schemata, one called "C" and another called "D". In the given order, "A" is associated with "C" and "B" is associated with "D". The ordering is as obvious as the matched cardinality.