My guess is that this noises you are hearing are the result of the drain lines expanding or contracting, especially with regards to the shower. RUnning hot water down the drain causes the pipes to expand, if they are rubbing on anything, that movement can be heard. Once the flow stops, they gradually return to their original size, again rubbing on something. Without tearing out the walls to find the offending point(s) and alleviating the contact points, you'll have to live with it. Stuffing insulation in the walls will help a little, but not much.
As the toilet finishes filling up, it might take a few moments for the bowl to equalize or stabilize to its desired level. Again, probably nothing you can do about it. Pretty much all toilets get overfilled...after the initial flush, the bowl fill function runs more water to them than they can take, so some continues to dribble out (just like overfilling a glass, once it is full, if you keep pouring, it overflows).