I really like the conceit of writing from the perspective of a diary. I don't think I've ever seen an epistolary novel where one of the correspondents is the actual "letter" itself. Sentient paper. It's a neat hook.
I feel like this story repeats itself too much. For example, the diary asking God for a heart. Repeating that a few times gives us the idea. No need to keep it up. Also the diary entries of looking out the window, and every day being awful. There is some progression of what they watch from the window, but not enough to warrant the space taken up. Also, the diary itself, who is sentient, doesn't comment on it, which is a missed opportunity to show the parallelism between diary and writer. I'd really want to hear what the diary has to say about each entry. That's the heart of the epistolary structure.
Brackets for internal dialogue and thoughts are probably the last option I would recommend. I have seen it done before with << >> tags, never [ ], but even then it is distracting. Here's a good primer on internal dialogue:
https://editorsmanual.com/articles/punctuate-dialogue/#thoughts