Ok I think it's best if you just delete everything and start fresh haha. You almost have it but it'll be easier and your computer won't have as many files on it. Basically if you can run the vanilla game you're good. It's just the process of getting the files in the right spot.
NOTE: You don't have to delete the port itself. Just the "Lucasarts" folder with all the game contents.
So follow the instructions in this video of installing the normal game (which it looks like you know how to do since you got it working before).
Then skip to 10:10 where I go through how to install DT2 and the 1.3 patch. Make sure you left the vanilla game in the folder you're running Wine too so it installs it all correctly for you. Then keep watching as I install the 1.3 patch. Make sure your file directory looks like how mine does in the video.
It should work for you after that. Let me know if it doesn't.
This is how your map selection screen should appear (minus the non-DT maps, those are just other addon maps I have).
[spoiler]
[/spoiler]
This is how the Galactic Conquest menu should look.
[spoiler]
[/spoiler]
Hope that helped.
NOTE: You don't have to delete the port itself. Just the "Lucasarts" folder with all the game contents.
So follow the instructions in this video of installing the normal game (which it looks like you know how to do since you got it working before).
Then skip to 10:10 where I go through how to install DT2 and the 1.3 patch. Make sure you left the vanilla game in the folder you're running Wine too so it installs it all correctly for you. Then keep watching as I install the 1.3 patch. Make sure your file directory looks like how mine does in the video.
It should work for you after that. Let me know if it doesn't.
This is how your map selection screen should appear (minus the non-DT maps, those are just other addon maps I have).
[spoiler]

This is how the Galactic Conquest menu should look.
[spoiler]

Hope that helped.