Super common with the L series engines. When setting the distributor spindle by mounting the oil pump the drive gear turns the spindle as it engages the crankshaft gear.
Suggestions:
- Yup, verify TDC with a piston stop - easiest way. Remember that the piston movement slows at the top of the crank arc so the crank can travel quite a few degrees with little movement shown on the piston. If you're really good you could probably ferret out TDC with a straw, pencil, screwdriver, etc. down the #1 spark plug hole, but piston stop will nail it when used correctly. Mark it correctly on the pulley if actual TDC doesn't match the indicator.
- The pictures in the FSM of correct spindle alignment cause more confusion than enlightenment. Also rarely do you get a good picture at a proper angle from anyone else. I've found it easier to set the approximate spindle position (with the top angled slightly left) and then set the distributor on temporarily and see where the rotor points. You can mark the distributor cap #1 wire position on the distributor body. At TDC, the rotor should be coming in contact with that #1 cap position. Notice that there is a wide arc to the rotor contact and quite a bit of adjustment in the distributor so what you think may be "close enough" may well be the exact thing you need.
I'm usually dyslectic about which way to adjust the spindle when putting up the oil pump and it generally takes me several tries so I never bolt it down with a four bolts. I use one bolt, snugged into position, until I'm pretty sure the spindle lines up correctly. There it helps to have a helper who knows how you want it to look after you've pushed it up...