The biggest remaining cause of a low score and slow loading pages after running SpeedBoost Ninja will be the other 3rd party apps that you have installed on your store. Try disabling the ones you have one by one and re-running SpeedBoost Ninja after removing each. (Caution: configurations and data for 3rd party may be lost.) Remember to refresh your Google PageSpeed Insights score too.
Once you have identified the culprit, either remove it entirely or switch to a different app that does the same thing.