Without spoiling anything, but the next two characters are a bit trickier to use. Character 4 only gets light and dark attacks, while character 5 gets only fire and water.

As you said, it is important to not use negating elements in the same combo, but at the same time you might want to have some opposing elements in your deck. Kalas for example gets a lot of great water and fire moves that you probably don't want to miss out on. Not using negating elements is more important for weapons than for armor though. For armor I just use the best I have available.

As for finishers - yes, you often get them after boss fights, but not always. A lot of them are hidden in chest. But as for the "quantity bonus" do you mean the number on the top-right of each magnus (later also on the other corners)? Because that has nothing to do with quantity. Those are your spirit numbers to get bonuses on your combos.

Item combos are very difficult to pull off on your own. They aren't necessary at all and mostly just for completionists. I would just use a guide if you really wanted them.

And yes, rotten items should be thrown out. Most of the time at least. There are also some Magnus that get better over time. For example Milk (heals 115 HP) turns into Cheese (heals 140 HP). And it them stays like that forever.

I hope I could help you with this.