Incrementally update code to handle new type checking versions

[stress-tess]

While working on PR #3638. I went through in and resolved most of the mypy issues, but I realized this would result in a massive PR since it would be making a lot of updates to satisfy mypy once typeguard is upgraded

If possible it would definitely be better to go through the files one by one and get them to the point where mypy is satisfied, so we can get more thorough reviews. We can then make the typeguard upgrade and re-enable the python 3.12 and 3.x workflows without needing a massive PR

This is a prerequisite for #3346

[stress-tess]

It does seem like typeguard has changed the functionality of it's check_type, so we may need to wrap it in order to be backwards compatible with out previous pinned version of mypy and I'd rather not require everyone jump ahead multiple versions