There are some issues with extiverse, I'm looking into it.
Update; after close to 10 hours working on this deep into the night I zeroed down on the issue. The API is functional again, but the site temporarily is no longer filtering on the latest Flarum version. I will need to do further investigation why exactly that filter is causing timeouts.
Update; fixed the issue, seemed versions and their compatibilities would be stored on every sync causing the table to fill up unnecessary and creating very long running queries when queried. I flushed the table and fixed the duplication issue.