Why do you want to use Shouko? Yeah it can bulk-tag anime but it doesn’t necessarily do a better job than Jellyfin with AniDB plugin. Also, it tends to hammer their API like an idiot and will get your user temp-banned or even perma-banned (depending on the size of your collection), while the Jellyfin plugin has rate limits.

I used it once when I was moving my collection to Jellyfin and I barely got my account back.

I would strongly suggest using just the regular Jellyfin plugins and adding titles to the directory in small batches and taking breaks if it stops recognizing them because it means the API is throttling you.