So if you acquire something really cool and want to keep it, you will have to keep the quest mod installed and active.
There is an odd and fun exception to this, but it only works if the cool item/s from your quest mod is a) not enchanted, or you have a mod that allows to reenchant items, and B) is something that can be enchanted, like clothing, weapons, armor...(and that's it really)
If you enchant that item yourself, the item created is a new form in your savegame, and will remain with your game after you uninstall the quest mod. If it uses models from the mod though, you'd better keep those in your game or you will have a big yellow square instead of an item when you wield it.
As for magic abilities coming from the mod (not spells, but passive abilities that appear in your 'active effects' menu), you should try to get rid of them before uninstalling the mod, because otherwise their effects can become stuck on your character. You can use a mod like RefScope to 'scan yourself' and get the formIDs of those abilities, removing them with 'Player.RemoveSpell' in the console if there is no easy way to remove them otherwise. Constant effect enchantments from gear should be okay, but still better to unequip any gear from the mod adding them before uninstalling to be on the safe side. Often (but not always) this is documented in the mod.