The chapel key is very near where you found the barometer in the central part of the house. The shed key is also nearby in the main house, close to the shed itself (very unexciting, though the chapel is more interesting!).
Might write up a little faq with hints to find the objects when I get some time. There's a built-in hint system, but it only gives a hint if you trigger the end and are missing a single one of the important items.