Hi @seanlandsman and sorry to hear about the trouble! I can indeed see an internal error trace for that deploy that reports that 43,383 files is “too many”. That doesn’t really line up with the number you mention, but it is anyway a good sign that a larger zipfile deploy also won’t work.
Could I suggest that you instead deploy with either the CLI (no need to zip up first): Get started with Netlify CLI | Netlify Docs or by committing all the files into a github repo?
The error was specifically in our zipfile handling, so either of those methods - not using a zip - should work better for a site of this size 