There is no 'original clause': that formulation is a useful fiction for understanding what the sentence means, not a historical fact.
But your paraphrases do represent how we interpret the clause. In this particular case, both paraphrases mean exactly the same thing, because wait is what we call an 'activity' verb: it has the lexical aspect "+DUR, -TEL", meaning that (other things being equal) its action lasts over time and does not necessarily end in a change of state. Consequently, the progressive construction doesn't really add anything which is not already implicit in the word itself.
However, paraphrasing I made some tea as I was making some tea changes the meaning of the main clause. Make is an 'accomplishment' verb, +DUR, +TEL, its action lasts over time and does end in a change of state—at the end of the process you have tea you can drink, whereas before and during the process you had at best some water and some tea leaves! Consequently, the simple past I made some tea implies 'perfective' viewpoint aspect (consult the same link)—the action was completed at the time you are talking about, while you were waiting for John. But the progressive version implies that you were still in the middle of the process when something else happened, which is presumably what you are going to tell us about next.