This is a far-out chance, Erinus, but you are trying to open the side door of the church, not the front one?
If Samuel read the letter, then it's put together correctly--there is supposed to be a small piece missing. Did you right click on the black rook and use it on the clothes you took from the garbage bin? There is one more thing to be put in the strange object--that might be what's holding you up.
If none of this works, you can send me a saved game and I'll try to see if I can figure out what's going on...
"Once you give up integrity, the rest is easy." Anonymous