"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
I don't see any separation clause there. Anyone else? Also that letter to Jefferson was more about people's fear of waking up one morning and finding out their new nation is suddenly Baptist, Methodist, or some other form of Protestant, or Catholic instead of being just Christian or Judeo-Christian based like everyone expected it to be."
It's not even explicitly stated in the first amendment. Maybe stop taking things too literally
"Also, also, where was your outrage when state was forcing churches to shut down in some way during Covid?"
They did shut down churches during the pandemic but they never stopped it from going online, and it was perfectly legal to do so.