Is there any special alignment for the black toothed wheel relative to the motor gear and say, window placement,up/down etc when reinstalling my old regulator? the big round/square pivot pin that the black toothed arms swings on came off so I pounded it back on so its secure and I am attempting to reinstall the whole assembly. Everything else looks okay. Or should I just buy a new(used) regulator?

My initial reaction is no, but let's think of this. Doesn't the motor operate in either direction without mecanical limits? I think so . The
black gear drives the scissor arms which are secured in to the window channel.

So the motor gear position is relative, the regulator black gear is absolute but it is tied to arm position in window channel.

Doing from memory so long winded way to say you're ok.

Hey in case this helps: did you know you can immobilize the window in any position.with one of your quick clamps (aka pipe clamp)? Just gently tighten its rubber pad to window at rear edge. Minimal pressure required.

john

On my 1997 the window travel is established by the electronics. When he window reaches full height the limit switch and door module shut it down. Same for the lower limit. Most likely there is no set position.