Well I beat Penance before I got to the stage where I was using Clear Spheres to erase and recreate, so no... But there's no need for a 'perfect grid'.
Before I realized I didn't need it, I was killing the Spherimorph thing and the Anything Eater for Luck/Fortune spheres and it took AAAAAGES. Thank god I didn't actually have to do that.
As far as just unlocking the spheres as they are, then yeah I've done that for everybody.