I'm in the process of rebuilding and ampedbike motor right now actually... So I can tell you what I know so far.
First off, I'm not surprised they stopped answering your emails. Ampedbikes is not exactly known for having the highest customer service... The reason I am rebuilding my motor is because I didn't want to send it back and then not hear from them for more than a month (I am speaking from personal experience here). I have learned the only way you can get an answer is to call them. And if you look at your kit cross eyed it voids the warranty. I don't mean to derail your thread though, so getting back on topic!
You won't be able to bypass the controller. The three phase wires going to the motor toggle on and off in a specific pattern, so just supplying raw power to the motor won't do any good.
When you hit the throttle... does it make any sound? Growl?
If it simply does nothing at all, then it could be the hall sensors, which is what went toast on mine. There are three hall sensors on your motor. They detect the position of the magnets, in order to know which coils to turn on next in order to pull the wheel around. If one of the hall sensors is toast, then it doesn't know what to do, so just sits there doing nothing. There is a plug with 5 wires in it. Red, Green, Blue, Yellow, Black. If you test between Red and Black, you should have 5 volts. When you spin the wheel, the voltage between Green and Black will toggle between 5 volts and 0 volts. The voltage between Blue and Black, and between Yellow and Black, will also toggle between 5 volts and 0 volts. If Green, Yellow, or Blue aren't toggling when you spin the wheel, then that means you have a dead hall sensor (in my case one was staying at 5v and another was being unreliable). They should toggle somewhere in the ballpark of 20 times per rotation, so turn the wheel slowly in order to see the jump on your meter. I really suggest testing these BEFORE you tear the motor open, as they are really hard to test once it's torn apart (I had to reassemble my motor in order to test them).
If a hall is dead, then it could be just that something is shorted out (perhaps mud, water, or rust is bridging wires). Or if they are truly dead for sure, you can buy new ones from Mouser. For most motors, you want Honeywell SS41
http://www.mouser.com/ProductDetail/Honeywell/SS41/?qs=sGAEpiMZZMtdU8v/CHkq39AvnkiVL6ci (there is debate about if the halls on my motor are more similar to SS41 or SS41F, but from what folks say it doesn't really matter and the SS41 will work fine).
In order to replace the hall sensors, you do need to open the wheel up. It's not the easiest thing ever, but it is quite doable.
It's easier if you just remove the wire side plate. If you remove the gear side plate, you have to first remove the gears.
To remove the wire side plate, remove all of the screws on that side. Mark the plate and the base of the motor with a sharpie, so you can line them back up right when you put it all together (some motors are not perfectly round, so you want the plate to match back up exactly right or it can rub on the inside). There is a fine seam, you want to pry that apart CAREFULLY. On my motor it was a bit hard to get a screwdriver in there, since the plate sat very smoothly against the motor and the paint didn't help either. But I put a small screwdriver in there, and tapped it LIGHTLY with a rubber mallet. You do NOT want to do it hard, because if it goes suddenly and you jam that screwdriver in there, you might mess things up bad. Once you can get a screwdriver in there, go around the plate loosening it up with the screwdriver. It might be hard to get it off since there is a bearing gripping the plate and the axle. Once you get the plate off you should be able to see the innards pretty well.
Here is a photo of what the inside of mine looked like when I took the first plate off:
If you want to remove the full stator in order to clean off rust, you need to remove the gear side plate too. For that you will want a freewheel tool (this can be a useful read about that
http://sheldonbrown.com/freewheels.html. Ampedbikes require a Park FR-1. However, the hole in the tool is not big enough to go over the huge axle of the motor, so you need to take a drill to the tool to widen the hole (or dremel tool). Once you get the gears off (which you should replace anyways if you are using the default Ampedbikes gears, they suck, and a shimano 6 speed hyperglide freewheel gear set fits great if you add a washer as a spacer), you then need to remove the sides of the motor. Once the plates are off, you can see the stator sitting inside of the motor. You need to remove that CAREFULLY. You don't want to hurt yourself, or the motor. It will be held in by some very strong magnetic pull, and I wouldn't be surprised if you could break a finger if you get it pinched in there.
My motor was wet and rusted inside, which was totally awesome.
If however, your hall sensors are doing just fine and all three signals are toggling on and off, then it's something else.
Other things that could be malfunctioning: Throttle, Controller, brake lever cutouts, battery.
To make it all easier, you could also get a tester from Lyen:
http://endless-sphere.com/forums/viewtopic.php?f=31&t=20413
In my experience, these things take a lot of tinkering and maintenance. However, most of the things you need to do on them are pretty easy. And remember, no one was born knowing how to work on these things, we are all learning as we go. So if you want to learn, you certainly can. And in my opinion, the tinkering is as fun as the riding.
I bought a Used Bike and Trailer @ the GoodWill for $275 it had an AMPEDBIKE REAR HUB MOTOR... the SLA batteries were in the trialer along with the controler 
!!!
and the next week I saw it @ the GOODWILL Mainstore for $75 Hell the batteries are worth that! 
SO i rebought this bike! yesterday I striped down all the wires and paid much attention to making sure everything was making good contact
