understanding electrical motor and force
would a capacitor from a microwave which is apx 9000uf at 2000v be
  able to work for this?


No, it would be completely useless. Despite its size, a microwave oven capacitor can only store a small amount of charge at 12V (certainly not enough to run a scooter motor). But even if you could somehow use this charge to boost the voltage, it still wouldn't magically increase the power available.


  as the existing wiring gets quite hot as is I fear overheating the
  motor and burning it up


The wiring is getting hot because the current draw is too high for it, and possibly also too high for the motor. 

You can reduce motor current by lowering the voltage (either using a lower voltage battery or by applying PWM) but that will also reduce torque. Motor torque is proportional to current. The only way to reduce current and increase torque is to gear the motor down. A gearbox (or belt and pulley set) allows the motor to spin faster so it draws less current, and also magnifies the output torque. It does this by trading rpm for torque, just like a lever trades distance for force.   

If no gear ratio provides the combination of torque and speed that you want then the motor simply isn't powerful enough to do the job. 

However in your case the limiting factor may actually be your batteries and wiring. Scooter motors are quite powerful, but draw a lot of current. Power = Volts x Amps, so a 12V 100W motor would need 8.3A to get maximum power. Most 18650 cells are rated for a maximum of 5A or less.