Good news! I install the new index.php and it then showed me the updates to be made. I clicked proceed and it stated that it successfully updated the database. Checking my si_sql_patchmanager shows 326 for my patch reference. I am able to log in to SI and use it as normal. Further more I am able to adjust my default pdf font in custom.config.ini.
I really appreciate the help! I am assuming the older index.php was not updating the sql database? My update had been from 2011 to 2019.2 and then master_2020.