MySQL to find all tables with a Full Text indexed column in them

I need to run a repair on all the tables in all my databases on my MySQL5 server because I have updated the MySQL full text search stopwords file.

Is there a query or command I can run to do this?

Yes, you just need to query the INFORMATION_SCHEMA.STATISTICS table:

SELECT TABLE_SCHEMA, TABLE_NAME
FROM information_schema.statistics
WHERE index_type LIKE 'FULLTEXT%'