So my Kodi has 90% of the episodes labeled wrong even though I have all the file names correct. Can I manually tell Kodi which episode goes with which file?
Kodi does not scrape in the incorrect order. The order comes from a combination of how you named and numbered the episode files compared to how they are listed at the scraper site.
In case you are not aware, TVDB has three listing orders- Aired Order, DVD Order and Absolute Order.
It is possible you had scraped Aired Order, but your files are saved as DVD Order, or in some combination using those three orders. And using XEN just happened to scrape correctly because you had the correct Order setting.