First of all I'd like to say I am not the creator or either mod/script I am a user of both and LOVE both. PAM works flawlessly for us on normal servers but SEWorldGen 2 messes with the positioning somehow and so I just wanted to share some insight on how I got things working again.
First just set things up as you normally would (I'm not going to talk about how to use the mod or script as the creators of both have already made good guides on both).
After set up if your miner is just not aligning correctly when trying to dock then all you have to do is help "guide" it back in. I tried many different configurations and this is what I found to work the best.
1. After setting the "Home Pos" move the ship out of the way and grind down the connector.
2. Then using conveyors extend out and build a new connector.
3. Build some slope blocks to help push the ship back to where it should be going when docking.


If it doesn't work to your liking just play around with it until it does. What might work for one ship may not work for another but I'm sure after reading and seeing this it should help you understand the concept.
Fly safe!