I am not an expert but I think you are explaining typical MCOR problems.
Try turning the key off and pumping the go pedal 20 times, and see if that has any affect on your issues.
As for the batteries they could be on their way out based on age, and what kind of care they received.
Check out this Battery information sticker if you have not already seen it:
http://www.buggiesgonewild.com/elect...batteries.html
Post up your individual and total pack voltages right after full charge and about 10-12 hours later.
Aflyer