Okay so I've tried testing that issue with "nex_skipStoryDefault" where it wouldn't let me start or load games and it's uh, not there anymore. I think the reason this is is because I replaced my entire Nexerelin installation to revert the jar modification. I believe I was using an outdated version of Nexerelin that didn't have "nex_skipStoryDefault" as a variable when i tried the test .jar.
But yeah anyways after that update loading and starting new games is fine with said test .jar, it also fixes the following fleets not attacking enemies you engage issue which is nice.
I do have another minor issue in that the integrated version checker says its not working even if I just use Nexerelin and its dependencies. I wonder if it's because I changed the name of all my mods (not IDs, just names) for sorting reasons?