If you have the motor I think you have it's rated RPM is ~2500 RPM at 36 vdc. With an 11 tooth gear on the motor and a 44 tooth gear on a 700c wheel the wheel would be turning at 625 RPM (2500/4) and with that diameter wheel would be doing around 50 MPH !!! Now you can go that fast on a bicycle but not without addressing the issue of aerodynamics, meaning some kind of fairing, etc. Using that fast gearing and making no attempt to address air drag, or any way to SLOWLY ramp up the speed, it's no wonder you were only able to do ~9 mph before the motor caught fire. You would need at least twice that much gear reduction to use the motor you have on a 29 inch wheel.
I have used and HIGHLY recommend the TNC Scooter 600W GEARED Motor - 36 Volts (Style: MY1020Z3) ($80.00) http://tncscooters.com/index.php?route= ... uct_id=337
Although the NO LOAD speed of the geared motor is rated at ~480 RPM, typical loaded RPM will run around 325 RPM. 325 RPM on a 700C wheel is around 25 MPH. Assuming 25 MPH sounds OK to you, you would need ONE TO ONE gearing (or close to it) between the motor and the 29 inch wheel. The smallest standard rear bicycle gear is 11 tooth. That's close enough to make the system work but I really don't like putting that much power and torque through that small a gear driving that large a wheel.
I ended up making an adapter for the motor and mounting a 16 tooth freewheel on the shaft of the motor. The primary reason I did this was so I could use standard bicycle chain (motor comes with a 10 tooth gear that takes much wider chain than standard bicycle chain) PLUS I wanted a few more teeth on the motor shaft. I used a heavy duty BMX chain due to the ~1 HP rating of the motor. The freewheel permitted the bike to be pedal driven without the gearbox on the motor turning. Not having a freewheel on the motor adds a LOT of drag to the system.
I'm not sure if you are locked in on driving the rear wheel directly with the motor, but I offer the following idea which has worked well for me.
The best way I have found to use this motor is to mount another crank gear on the opposite side of the crank and run the motor power through the gear system along with the human power. The one disadvantage of this is the pedals will go around any time the motor is spinning unless you go to some kind of crank arm freewheel system. This was not an issue for me since I ALWAYS pedal when I am riding.
My cadence runs around 100 RPM. The motor runs around 325 RPM under load and I have a 16 tooth gear on it. This means I needed approx. a 3 to 1 gear reduction. So I mounted a 48 tooth chain wheel on the opposite side of the crank. With this gearing the cranks turn at 108 RPM full throttle and my speed on the road is be dependent on what gears I have selected with the front and rear Derailleurs. If your natural cadence is slower than 100 RPM you would simply use the motor to drive a larger chain wheel but finding chain wheels much larger than 56 can be difficult.
Top speed on this system with the gearing I had and a cadence of 100 was 43 MPH on level road. Typical cruising speed was 28 to 32 MPH. This was with a 20 inch (406) BMX wheel with a 2.25 inch tire. In the lowest gear this system had so much torque that I managed to spin the rim inside the tire which cut the valve stem off resulting in an instant flat tire. This issue can be greatly reduced by using tires rated for the task at hand and keeping an eye on tire pressure. I doubt you will run into this issue with 700c wheels as that is a higher speed lower torque wheel than something like a 20 inch (406) wheel but will give you some idea of what this motor is capable of when properly geared to the wheel.
Right now I am using one of these geared motors to turn a 10 foot propeller for some aircraft experiments. I am using a gear reduction of 2 to 1 meaning the motor is turning at approx. 320 RPM and the prop is spinning around 160 RPM. Current is running around 20 amps at 36 to 42 VDC for a power level of 720 to 840 watts. The motor will do this all day. I have used higher voltages on this motor and have seen power output levels in the 2 to 3 HP range for S-H-O-R-T periods of time as the motor will overheat if you continue to run it above it's rating. You already appear to have some experience with that issue...
I have found TNC Scooters VERY responsive in the past to both Email and telephone. BUT, keep in mind they are a SCOOTER store and tend to shy away from non standard use of their products such as mounting a scooter motor on a bicycle and when confronted with questions of this type may try to avoid becoming involved as they have NO EXPERIENCE with any of their products outside what they were intended to be used for....
PS - Had the current limit of your controller been set to something more appropriate for this motor you may not have experienced the meltdown that occurred. However, the gearing you are trying to use is not even in the ball park for the motor and wheel diameter you are trying to use and is equivalent to trying to run the motor in a stalled or locked rotor condition.
Under those conditions current limiting may or may not prevent a meltdown depending on how long power is applied to the motor. ALWAYS keep an eye on temperature when testing a new system. If you can't touch and keep your hand on the motor, it's TOO HOT !!!