try raising the pole pieces under the g string a tad until the output evens out. That's why they are adjustable.
try it under the E as well. I am unsure as to *why* the open E sounds less so than a fretted note on the same string, but are we speaking acoustically, or amplified? If it's amplified, it could be many variables, not limited to nut material / winding count / break angle over the nut, etc... one more reason I'm a fan of zero frets...
