a- Take this time to consider migrating to Postgres . I would never trust anything financial or critical to MySQL. Their integrity blows.
b- If you are staying in MySQL, MAKE SURE that you are using AT LEAST v5.0 so you can enable 'TRADITIONAL' mode.
TRADITIONAL mode does some crazy things-- like require text to be valid for the field you stuff it in. Otherwise, mysql will start doing things like trimming and inserting the largest substring of your field it can fit into a column, without calling an error. ( real databases call fatal errors on stuff like that ). Mysql will also change data types without telling you, along with a long list of horrendous things. It was built for speed and widespread use-- not for correctness of data.
Comment on Re: Verify database consistency after merge
I'm aware that there are many issues with MySQL. But as with any tool, used appropriately, it works fine for this particular application. I perform analysis on the data and are much more dependent on small data size and raw speed than transactional behavior. MySQL has proven ideal for this.