You are going to have to tell me how to do it rather than telling me to do it, as I aren't familiar with programming. "Just" put it in a mission you say. If only it was so easy for me, I would had done it already.
I've been asking for the sim to be much more options for a while now so that it is easier to test out builds.
Ok man, let's get you in a Prometheus in the simplest way, take you less than 2 minutes:
1.Run Starsector with any save,
2.Open your fleet and pick a ship you don't want any more, strip it and rename it something funny, like "1122334455", and then save game
3.Go to your save folder and open campaign.xml with a word pad
4. Press Ctrl+F and search for that funny ship name, "1122334455" in this case. You should find the funny name in a block of text like this, with the ship type defined with
hId one or two lines below the ship name:
<FMmbr z="138215" o="1" sid="buffalo2_FS" sN="1122334455" t="SHIP" iF="false" id="1e92cf" sUN="false" civ="false" cCiv="false">
<savedVariant z="138216" hId="hermes" v="0" c="0" hVId="buffalo2_FS" vDN="Support" s="REFIT" mAAW="true" gV="true">
5.Change the
hId="hermes" or whatever, to
hId="prometheus2" 6. Save the campaign file, and load it up in game, and the ship you didn't want any more will turn into a Prometheus Mk2