"Did you intend on writing it, initially?"
Yes. But when I got to the part where Cat read "My Beloved Wife" on the envelope and she broke down, I knew it wouldn't work to write it out.
"Do you ever?"
Do I intend to write it now, do you mean? If so, the answer is no. It was either going to be revealed in the scene, which ended up not happening, or the letter stays sealed. Even I don't know everything that's in it
"I was wondering what happened to that box. It wasn't mentioned after she fell asleep. Did Bones find it? Did they leave it at that house?"
Bones found it and gave it back to Mencheres. Mencheres brought it with him when they left the house after the battle.