If you call the ship and get this message "You must register this ship first!" for all your ships except the Frontier, you got a weird vanilla bug that is exposed by this mod.
This bug is NOT this mod fault!
It's unknown for now, but it happens to some people, even without ever having the game modded before. It can cause many side effects with quests involving your ship, like teleporting you in unwanted places after entering your ship or making your ship door inaccessible.

You can fix it with this script I made specifically to address this issue.

Install the 'Data' folder of this .zip as a regular script mod. Exactly like "Call Your Ship" mod.
After you've installed and booted up the game, load your bugged save then open console and type:

cgf "ShipFix.GetHomeShipID"


then the console should point to the ship you're current using and in the console you should see also "prid YOURSHIPHEXID"
after that, use this other command:

cgf "ShipFix.GetQuestShipID"

should do the same but for the ship the game is pointing to for quests, and should say it's the Frontier. The ID should also look different.

 
Now, use this command to fix the save:

cgf "ShipFix.ResetShip"

a popup notification should say "Ship Reset".
Then try again the first two commands and you should see that the two IDs are the same and match your current ship.


Finally, test "Call Your Ship" mod again, if everything went good, it should work as inteded.

Now you can save and it will be permanently fixed :)


NOTE: If for some reason the bug shows up again, you can use this script whenever you need it.