I guess my first question would be: why not take it to the dealer that sold it to you for repair, or return? I would expect a warranty of some type, even on a used vehicle.
A 72v charger is only useful for a 72v pack. if you use it on a 36v pack, you will damage the batteries. (unless it is a charger that autodetects the voltage of the pack attached to it, but I havent' seen one of those for SLA). If other stuff on the bike (like DC-DC converters for lights or whatever) is connected to the battery when you hook up that charger, it could also damage those, if they are not rated for that.
FWIW, according to the specs on the page you link, it *is* 72V, not 36V:
Motor / Power:1500W
Battery Capacity:Lead-acid 72V 20Ah
Charge Time:8-10 Hrs
Chargeer Life:250 or more
Brakes:Front Disc, Rear Drum
Climbing Ability:20 Degrees or more
Max Speed:>28 Mph
So if it only had a 36V charger, and a 72V battery, there must be some electronics in there that switch the batteries into a 36V configuration in order to charge them, and back to 72V to run. But if not, then a 36V charger couldn't be charging it correctly (more likley would actually discharge the battery and/or damage the charger). So either the specs are wrong on the linked page, the wrong charger was supplied, or someone has already rebuilt this scooter with different stuff than it came with originally.
Notes: If you use a 72V controller on only 36v, it may work, as long as it does not have an LVC to cause it to shut off below a voltage that is above your pack's actual LVC.
If you use a 72V controller and 72V battery pack on a motor that formerly used only half that, it will likely cause great heating of the motor if you run it at full throttle, and during startups or on hills.
It may also cause great heating of the motor to use a controller that can output a higher current than the original, depending on start/stop and terrain conditions, as well as speed you ride at and how you use the throttle.
If the wiring failure that caused the flash and burned the wire up did not destroy anything in the controller, you can simply replace that wire, but you need to know where it went and where it should go. Where was that wire connected to when it burned, and what is is it supposed to do?
Most throttles work with most controllers, but you may have to figure out which wire goes where, as the connectors may not be wired the same even if they are the same colors and connector shells.
Some scooters have separate electronics for all the non-motor stuff, and some of them it is all integrated. You'd have to trace out all your wiring to find out whcih yours is.
Since it's brushless, and it worked on a different controller, it could be hall sensors--either a bad sensor or more likely a bad connection to one. Those can cause some horrible noises as the controller tries to commutate the motor but leave it unable to sync rotation of motor with signals it's putting out.
Could be the controller instead, blown FETs or broken wires/etc inside the controller.
There are a number of threads around ES on troubleshooting motor problems, which include how to test hall sensors, and how to test controller FETs, and how to test various connections. May take a bit of searching to find them, though, as I don't have any direct links.
It's still a work in progress, but there may also be articles or links to them in the ES Wiki: http://www.endless-sphere.com/w/index.php/Main_Page
The good news is that there are quite a few ESers in San Diego, and perhaps one of them can physically come by and help. But you might want to put htat location in your profile, as I only found that on your blog.