Yeah, redoing the system table will result in trouble. Drupal runs the install functions for modules when they're enabled w/ no install history in the system table. For the store module, that means bringing in the U.S. and Canada zones again. I'd go to your country settings and remove everything and re-enable the countries.

And the lag time is due to an AJAX call. I think a "loading" icon would be appropriate there. I'll see if I can cook one up.