For the overflow the only thing I can think of is to put some snails in there to eat the debris. An alternative to the large slightly dirty piece is to get some kind of foamy pre-filter and put it on the bottom to catch the drops before they can make noise. You could also try to jury rig a funnel and tube and bypass the tower entirely. In all honesty, I doubt that the decaying debris will cause an ammonia spike, in fact it may even help the bacteria increase in number so they can handle more/larger fish faster.