Upgrade to OJS 3.3.0.6 foreign key constraint failure

I’m attempting to upgrade from 3.2.0.1 to 3.3.0.8 and have had the same issue with some of my tables being MYISAM while most of them were InnoDB. I modfied all of the MYISAM tables in our production database and then copied the entire DB into my separate clone to be used for upgrading. Alan Smecher had stated elsewhere that if you run into an error during the upgrade process, you need recopy the entire DB and start over from the beginning, which is what I did. But when I restarted to upgrade process, but I still get the same error:
SQLSTATE[42S22]: Column not found: 1054 Unknown column ‘url’ in ‘field list’ (SQL: select url, navigation_menu_item_id from navigation_menu_items where context_id = 1)
Any idea of what I should do about this?

Please see my more detailed posting here.