Usage of "must have" in past tenses

There is no alternative to "must have". All modals, without exception, are always followed by the bare infinitive. I could write several pages on why this might be so, but no one would be any the wiser. Suffice it to say that some things should simply be learned as properties of the language. Modal + Infinitive is one such instance.

In the particular case of "must", you might want to consider that in expressing an assumption the assumption itself is always formulated (if not expressed) in the present. "John had thought". Is a report on a past event about a prior event. Thus, past perfect.

"John must have thought" is an assumption formulated in the present about a past event. A perfect case for the present perfect, which serves to bridge the present and the past. One, in fact, is going one tense back, from present when the observation of what John must have been thinking was first articulated to past (when John in fact had been thinking something).

In this case, "must" has taken us to a meta-level of sorts: The observer is observing the observer.

Full disclosure: I'm not a professional linguist or philologist. Just a guy who asks a lot of questions and is a life-long learner. So, I will be offering what little I can contribute in hopes that it helps others.

As a writer and a native American-English speaker I would say that must have is the most appropriate and common construction for this type of situation (although I cannot comment on its technical/grammatical correctness).

In your example:

The truth was, Frank was not that much taller than Maria; she must somehow had made herself appear shorter

It would look better and, I think, convey the same meaning to write thusly:

The truth was, Frank was not that much taller than Maria; she must have somehow made herself appear shorter

Here's another example:

When he was stationed in Marrakesh during the War, Frank used to walk down to the shore, stand in the breeze with his toes caressing the sand, and recall how Maria would always say "I love you" in that soft, whispery way.

In this example, the narrator refers to something Frank used to do in the past (think about Maria on the beach), and what he thought about was something that happened in the past relative to his perspective in this past circumstance in Marrakesh.

Here's another example just for fun:

When Elvis flew B1-Bombers during the war he would put the bird on autopilot on occasion and play up to three hands of gin rummy with his copilot, Bob "Booger" Matthisen. Bob couldn't help but regale Mr. Presley with tales of his time as a deep sea fisherman and had to fight off all manner of beasts including great whites and giant squid.

There are just two examples of how you can convey what I was call nested levels of past referencing.