Another possibility (from your description) is that the distributor cap was previous rewired to compensate for the gear being turned wrong. But if the engine ran, and the rotor pointed to the terminal that was actually connected to #1, and the engine has not been turned since then; it pretty much has to be #1 on compression.
BTW, the illustration above is from the workshop manual.
Just to show the strange things that can happen, my Dad's TR3A had the gear turned wrong and the wires moved to compensate when he/I bought it. (I found the car, Dad paid for it.) We went for many years with it wrong, never noticed there was a problem. Then I found another TR3A and bought it for myself. Trying to make it run, one of the first things I did was move the "known good" cap & wires from Dad's car. (The ones on my car were extremely ratty, with big cracks in the insulation and so on.) My buddy and I spent two whole days in the snow and cold trying to get my TR3A to run. (It was basically abandoned in the back yard of an empty house, we were hoping to make it run to get it home.) Finally gave up and towed it home on a rope, then spent another day trying to figure out why the $&! engine would fire but not run. Finally the light dawned and I stuck the old cap & wires back on; it of course fired up promptly.