Are extra classes and extra research worth it?
A better GRE score is worth more than a 2nd online independent study project especially if you expect good letters of recommendation.

Think of it this way:  online 4.0GPA + bad GRE score = looks fishy  =  you might not be as good as claimed and maybe you cheated your way through the online education system ("outsourcing" online classes is not uncommon these days).  then it won't matter how many independent study projects you did.