Your batteries aren't likely the source of the lack of amperage going to the motor. Its probably the controller. Most of them have thermal limiters so when you mash on the throttle and heat it up it limits amp output to stop from frying itself. You need to find a way to cool the controller, or get one that is made to handle higher amperage. When you are looking at controllers, you need to not just look at peak output, but at the different ratings over time (5 min rating, 30 min rating, etc).
Sorry to hear it didn't work out, but I have to agree with Frank. Unless you have a pure EV mode for cruising, you're not going to see much of any benefit because your engine is already way oversized for cruising efficiently.
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