Based on @AlexPoole and @EdGibbs comments, I decided to add a bunch more debug statements. It turns out the method was being recursively called with a different sql "suffix" later on in the program if certain conditions were met. The suffix was not updated with the necessary parenthesis for the new ROWNUM wrapping the statement. So although the ORA-00907 can be thrown for many different formatting problems, it was in fact a right parenthesis that was causing me problems :P
The prefix and suffix seems like a weird pattern in this code base for creating sql queries. I'm thinking of getting rid of this and refactoring so queries don't have to be built like that. Any advice??
So for anyone else who runs into this Oracle error, I would suggest logging the sql statement you are generating and play around with it in SQL Developer. If it works in there, but not in your application, your code is probably doing something funky :P