What I did in EIC - with the help of another forum member - was combining two things.
First thing you need to do is to save a copy of the Shiptypes.ini file somewhere. If you still have the original modding download at your computer, you can fine an original there, so there's no need to create the back-up.
It would however be a very good idea to create back-ups of your saved games. Just to make sure nothing goes wrong with them the moment the modded files creates a problem.
Second you need to create the new ship type in the "shiptype.ini file".
That new ship type needs another name; i.e. Kraier Mk II and all stats of the original Kraier.
When you've done that, you can start altering the stats of the Kraier Mk II, like in creasing length, with, cargo space, etc.
The third thing you need to do is to link the image of the Crayer - Kraier - to the Kraier Mk II stats. I'm not sure where to find that, but it might be in the Shiptype.ini file as well.
And finally, you have to decide when the ship got available to you. Since only the Crayer, Snaikka and Cog are available at the start, you might want to add the improved ships to the research list of the university.
I.e; the improved ships come available after you have researched the Holk.