Can I consolidate multiple MYSQL databases into one database via a script?
I found a solution to my problem. 
I wrote a select statement from the information_schema database that pulls all of the databases and their tables. I then ran these commands via CLI. 

select concat('alter table ', table_schema, '.', table_name, ' rename NEWDB.', table_schema, '_', table_name, ';') from tables

Thanks for the advice, help.
Hopefully this helps someone in the future.