I have been pouring over all the data I have collected, such as range estimations, AMP draw at different speeds, top speed and all these hills. I them made a conclusion and took it to the electric vehicle teacher and he agreed: my controller is way underpowered.
Actually, I learned that my K99-4007 was actually quite fine for the Civic with the blower cooler and proper gear selection. It was my controller limiting the acceleration and AMP draw to the motor. Which makes sense because my controller couldn't provide the continuous power required to maintain hills, and I only need to higher AMPS for a few seconds.
So now I know it's the controller, it's on the top of my EV list of things to buy. I am still working on getting a plug at school, but I really need the upgrade controller before driving it there. I hope to have the new controller by the end of August, before the semester starts up again.