There’s really no rocket science here. Yes your window is to low if it’s hit a mechanical stop. The top edge of the window should match the top edge of the quarter vent frame. The spacing between the top of the window and rain gutter should be even along the top with a similar even gap between the rear window edge and the B pillar. It should look like this.
The window tilt should be adjusted so there’s just enough pressure to close up air gaps and keep water out. Anything more will add resistance to door closure with the window up. I’ve never seen a door gasket wear at the top like yours so if that is due to the windows bearing hard pressure on the gasket, you’ll need to make an adjustment.
The best advice is to search the archives for information on door gasket issues and replacement. Door closure and latching issues are a common problem when replacing the gaskets.