It all depends on what the issue is. If it is simply that the wiki minigame mod is not loading when CCSE is active, it might need to get a check to force it to wait for CCSE to fully load.

Check out the documentation: https://klattmose.github.io/CookieClicker/CCSE-POCs/
Use the method described under 'to wait for CCSE to finish loading before continuing to load your mod'

If the issue is more complex, it might need to be re-written as a CCSE mini-game.
Compare your mini game code with the CCSE casino mini-game: https://github.com/klattmose/klattmose.github.io/blob/master/CookieClicker/minigameCasino.js