Hmm, step 0, eh, I don't know anything about being able swap ships out but I'll tell you what I know.
When you extract the files from the game, most of the data can be found in START.DOL. I'm able to see values of certain things opening this file with HEX Workshop, as can be seen in an earlier post of mine:
When you find the item you're looking for, you pretty much have to guess what each value affects what and what each value stands for. For example, in the screenshot above, you can see that all items under the third "0" column is the Attack statistic for ship cannons. The attack for the "Main Cannon" can be viewed on the right hand side, where it says "35" at int16. The 35 statistic should be editable, so I can change it to 999 if I want the Main Cannon to have 999 attack.
I have no idea how to repackage a game back into an iso, though! It would be neat to learn how to do this, considering I recently learned about enemy formations. It should be possible to make any enemy formation, such as 8 Elcians, or a party of Vyse, Drachma, Enrique, and GIlder in any scripted encounter! I think it would be neat!