Is it really stomach discomfort though? At a pH above 5 you’re still way above what a healthy stomach should be. Perhaps it was your esophagus that hurt?
For sure, I was using stomach discomfort as a broad euphemism to mean the overall unpleasantness I experienced from drinking coffee compared to days when I abstained. Anecdotally, I have a friend who quit coffee for similar reasons who also took up drinking AeroPress brew successfully.
How long do you typically leave between adding the hot water and plunging the aeropress?
Around 15 seconds. This is on the low end of extraction time, official instructions say between 10-30 seconds, although it's really to your preference, and some people prefer a minute or longer.
With drip coffee or french press, you're looking at steeping times around 3 to 5 minutes.