I have quite recently started a new game, where I among my selected mods have included my own Mod 'the dwemer society' . Some might remembering me working on it a few years ago. It was never finished, but it does include around 20 quests, so I thought it might be interesting to include it in my game and see how it works.

I have found some minor errors like wrong spelling, overlapping meshes and some things, that could be made smarter, which I would like to correct in my game.

But I'm wondering, if these changes will cause major problems to my current game. I will probably need to clean them with wrye Mash, but should I expect the game to work with no problems after that, or would I need to set ud a separate installation for making changes in my mod (needlessly to say, I would prefere to make the changes in my current game).

You can just make a backup save if you really don't want to start over. I would suggest cleaning the mod with enchanted editor and/or tes3cmd after you edit it in the construction set though.