Thanks for the responses. I ended up reinstalling the entire blog (thankfully we weren’t too far in). In this process I seem to have figured out what was going on.
This is an example permalink for a post: https://jordymcnamara.com/blog/index.php/uncategorized/trial-and-error/
For some reason there is an index.php in there (need it for the RSS feed as well) and it doesn’t work without it. Anyone know why I have this in there? Better yet, do you know how I can remove it without destroying my entire blog again?