[SkinnyG]

~Where~ the rotor and #post are don't matter as far as quality of running. If the rotor, where you have it in the first pic, has THAT post going to cylinder #1, then it'll work. If it's running rough, AND THE BASE TIMING IS SET CORRECTLY, it's not because the rotor is pointing somewhere else.

The rotor is supposed to pointing AT cylinder #1 at TDC of compression. #1 wire should be coming off the post just left of front and center on the cap. With the cap off, the rotor is POINTING AT #1. This is just the standard way of doing it; it's easier to troubleshoot if it's set up correctly and "as expected."

As LVPhotos says - you might have the rotor where it is in you photo if you are at Top Dead Center (TDC) of Exhaust, in which case it WILL be pointing to the right location in the next rotation and #1 is at TDC of compression.

BUT: which post you use to fire #1, assuming the rotor is at that post, won't affect how the engine runs, all else being equal. If the timing is correct, your issue lies elsewhere.