This is a link to the git repo's bot schema files:
https://github.com/EQEmu/Server/tree.../bots/required
I would start with the oldest file and go through each one to ensure that the table/view/function was added and then move on.
You shouldn't need to verify all of the data entries..just make sure that if it's a schema addition/change, that it is there. Should only take about 5 minutes
if you do it manually.
I'm not sure what the problem is..but, it did work correctly when I implemented the versioning system.
If nothing else, drop the bots schema and apply 2015_09_30_bots.sql manually, then run the update script and select '4' again.
EDIT: Looking at your update script errors, you are definitely missing 'base' schema...