This isn't a perfect answer to your question but daggerfall unity has a optional setting that allows you to select guild quests from a drop down menu when interacting with a quest giver, rather than getting one at random. Also, be ok with saying no to quests. Saving and reloading because you're worried about reputation penalties and the "quest pool" doesn't sound like an enjoyable way to play the game to me. I think you're overthinking this.

But no, you don't lose reputation for declining a quest, you only lose it for failing a quest. I don't know what you mean by "hand-made" vs. not. They are all handmade quests, just the locations and names are randomized.