Wow, thank you platypus and spaghetti, so much helpful stuff to think about.

To answer some of your questions: I would say it's mostly phonetic although sometimes the phonemes are a bit mixed up (f instead of th or something like that, especially at the ends of words). Spelling is consistent within a document but not always day to day. He reads out loud mostly happily, although he definitely prefers for me to read to him and likes for me to reread things to him even if he's read them before. I feel like in general he's more fluent on more difficult texts, surprisingly. Part of that's because when he's reading easy books he tends to use silly voices and stuff like that. He definitely misses a lot of small words and 'fills in' things that he thinks makes sense rather than reading what's on the page sometimes. That's my most common 'correction' when I'm reading with him. It's usually small words that he knows like 'for' and 'from' that don't really change the meaning of the sentence. I haven't had him read a list of nonsense words or anything like that so I'll have to check on that. He definitely can sound out long words but does tend to make some big jumps sometime and just guess.

For 4 & 5, he doesn't know the keyboard well enough to type and definitely misspells things that way as well, although he has very little experience with it yet. For 5 (mishearing), that aspect of things has improved a ton since he got his eartubes last year. I'll need to pay attention to that over the next couple of weeks though. He is currently in speech therapy at his school for pronunciation issues ('r' and 'l' and 'sh' and 'th').

The dysgraphia angle is a definite possibility, since writing is by far his largest difficulty in school. I'll look into the reading and spelling programs you've been using as well. Thank you so much for all of your input and thoughts, it's very appreciated!