Far as I know missing textures won't result in the game crashing.
The objects that use it would just appear gray.
You are replacing ships right?
If I were you I would just swap out the GM files.
Unless you want both the old ships and the PotC/TEHO ones I don't see a reason to go through the process of adding them in the code.
Less things to go wrong too.
Edit: Also if you want to edit the shpis stats you can edit the ones already there.
End of edit
Maybe you should consider uploading your files related to the ship.
Yep, this would be really helpful.
They should be in your main directory.
"C:\Games\CoAS\" or something like that.