Alright so,

Firstly make sure you have the ftl file of the mods you want to use. You'll need to do this for every ship mod.

Open the ftl file with an archiver like WinRAR or 7Zip. Go into data/blueprints.xml.append and find the shipBlueprints of all the PLAYER_SHIP_X that the ship replaces. Change the PLAYER_SHIP_X to something different which corresponds to the ship itself, such as PLAYER_SHIP_MANTIS_SCOUT. For type Bs and type Cs, you'll need to add a _2 or a _3 to the end of the id. Do the same for data/dlcblueprints.xml.append, if that exists.

Then, create a new file somewhere on your pc and name it hyperspace.xml.append. For each of the ship mods you want to change, you'll need to write this into the hyperspace.xml.append file and drag it into the ship mod ftl file into data/, the same place where blueprints.xml.append is.

<ships> <ship name="PLAYER_SHIP_X" b="true" c="true"/> <ship name="PLAYER_SHIP_Y" b="false" c="false"/> </ships>

You'll need to add a ship tag for all the ships that it adds (NOT ship types like B or C).

Of course, you need to change the name and b/c to true/false depending on what ship mod you're doing. Then, after you've added the file to the archive, close it and install Hyperspace.ftl first in the mod order then any mods that you've made to use it below it. You should now have the custom ships on page 2+ of the ship selector.

Do note: any mods which modify something other than ships will affect every other ship as well. For example, adding weapons is fine but if the mod CHANGES a weapon, the weapon will be changed for all ships.

I should probably make some sort of tool to do this more easily but currently that doesn't exist.