You are welcome, I figure if I find out the answer it is only right to post the solution for other people. Technically I caused my own problem, but glad I remembered what potentially caused it.
Another thing is: If you actually have this problem, dumping an SQL File and swapping the lower_case_table_names to 1, delete the tables, then execute the sql file... this will store the table names as lower case. Just remember to swap all the queries to lowercase in this situation, just as a precaution. This will swap all the Foreign Keys to the lower case, the tables to the lower case, and everything works then. No need to remove Foreign Keys, especially if you made the booboo of disabling Foreign Key checks instead of resolving the originating problem like I did lol.