I took a look at the commit and i think there are only two small things that might need changed. Since this Jira issue is still open you can go ahead and resolve it once you've made and committed these changes.
The first is that in the EN_DOC_HDR_T.table.ddl file you should go ahead and just delete the columns instead of commenting out the lines with those fields. We have the SVN history of the file if we need to revert so you should be safe to remove the lines and use the dball.groovy script to regenerate the bootstrap files. Also on a side note, i don't know if the dball.groovy instructions say to refresh your project in eclipse before syncing the master bootstrap files but that is one thing you do need to do. That could have been the odd things you were seeing before with them.
The only other thing i did see was that you had a schema name prefixing the table names in your kew-upgrade-0.9.3-to-0.9.4.sql. We try to do all our DDL and SQL assuming it will be run as the schema owner since we can't regulate what schema individual clients may use.
Let us know if you have any questions.