Side to side.
Here is a trick I used for those. I left them loose and closed the doors with windows down a bit then I raised the window then aligned the "bumpers" side seals.
When you do get your seals. try this, put the top on without the front and rear seals and of course after adjusting the side seals first. see how the quarter windows sit with the windows down. they should be even on both sides and as you look from the side.
If those quarter windows are to far inward, they can damage the door and paint at the weakest point where the window and quarter window meet at the bottom. So take care. There should be little to no effort when pulling the trigger of the door handle. Too much resistance on the trigger will eventual break the trigger
or the inside door release handle.
Can you post a video of you opening and closing the door? I would be listening for the Porsche "PING".
I will post a video as I promised couple of other Pelican Targas