New motor backfiring through carb

If it was 180 degrees out then wouldn’t one of the lines not be lining up. I drew one line at 12 o’clock and another at 3. If it was 180 out wouldn’t the one at 3 be at 9 o’clock?

You can draw lines anywhere you want on the housing, but if that shaft rotated while you had it out your timing is now wrong. Plus, if the intermediate shaft wasn't put back in exactly the same, then the distributor shaft HAD to turn to get the distributor back in and for your marks to line up.