@jp I know this thread is a couple of years old, but I found it while reading about waking up in the middle of the night after menopause, so hopefully it helps you or anyone else who lands here.
The blood sugar and digestion points above are good ones. Something else that might be worth looking at, if you haven’t already, is a full hormone panel. One drop of Progest-E for a few days is a pretty small amount, so it may not tell you much either way. Progesterone, thyroid and cortisol can all play a part in that 2 to 3am waking, and having actual numbers makes it easier to know what to adjust instead of guessing.
If any levels do come back low, a provider can go over the different options, like creams, capsules or hormone pellet therapy for women, depending on what suits you. Not every option works for everyone, but it helps to know what’s out there.
Hope your sleep has settled down since then!