5.2 Magnum Distributor Question

The important thing is...at top dead center the rotor is firing on the wire that leads to #1 plug. Then follows the normal firing order 18436572.

Doesn't really matter where it's pointing as long as it's firing #1 at Top Dead Center , but the vacuum advance can hit the firewall or block if it's not centered.

Yes, you can re-clock the intermediate shaft so the slot lines up. Not all distributors are clocked the same way.
I haven't taken the old dizzy out yet, so everything is currently how it left the factory. So the drive should not be out of sync.

I'm just going to remove the factory unit and install the new one identical to how the old one comes out.