ElectricMotorcycleForum.com

Have you tried connecting your throttle directly to the alltrax controller?  Unplug the small spade connectors 2 and 3 (on the alltrax) and run two new wires from the throttle.  Those two wires are reversible (no polarity) since the throttle is a potentiometer.  Try leaving the number 1 wire from the main bike board so your safeties will still work.  That's the permission to run terminal (key switch, etc). 

If the bike is on a test stand you could use a 5k ohm potentiometer too.  If the main bike board won't give you a green light on the Alltrax, you could supply your own signal (like the pack voltage) to the number one spade connector.  This will bypass the main bike board for testing purposes but only do this with the bike on a test stand.

You're lucky Zero is working with you on this problem.  My 2010 DS is still under warranty (it was bought new in Dec 2011) and it needs a new Alltrax controller and Zero has completely written me off.  I guess they think I'm trying to get a free controller out of them.  Yeah, like I'm going to leave my bike in pieces all over my garage so I can score a free controller!  And get this - my bike has been down since October 2012!

I have a 2010 DS with the same Agni motor and same battery pack although slightly smaller than the 2011 and commute 17 miles to work on Hwy 880 in the East Bay.  Most of that 17 miles is all freeway and I have to do it in the slow lane to cover this distance.  By the time I get to my exit my fuel gauge is blinking"empty" mostly due to the heavy amp draw (usually 150 to 200 amps) from my freeway run which brings the pack voltage way down temporarily playing havoc with the fuel gauge.  Then when I get to work 6 blocks from the freeway, my gauge goes back up to "half tank".   With that "half tank" I might be able to make the return trip home but only at something like 25 mph on city streets.  Luckly I can charge at work.  The 2011 Zero S should do better with it's lower profile (than the DS) and the slightly larger battery pack.  I've had my DS at 80 mph before but can't do it for 17 miles.  Ten miles, mmaayybbee.

Still, I prefer riding the bike over taking my tornado maker (car) to work.  The car takes about a gallon of gas each day(about $4) verse a few pennies for the Zero.

An example of the ridiculousness of the study:
"claiming that a Prius will last only 109,000 miles, well below the stated "industry straight average" of 178,739 miles—not to mention the whopping 379,000 miles ascribed to the Hummer H1."

I'm in big trouble.  My '07 prius has over 107,000 miles and according to these guys the car will die at 109,000 miles.   The funny thing is the car drives almost like new, just a little more "broken in".  The car has been very reliable.  I only had to replace a water pump and that I bought online for $33 for a toyota manufactured pump plus $8 shipping (I know because I just did it last month ).  The only other things are routine maintenance items like oil changes, etc.  No brake work because of regen.

So Harlan will have a FX frame and a XU motor left over.  I'm assuming he'll put these parts together and come up with a XUF bike.  A bike that would be great for a tall person who has an aversion to speed.

+1 on the e-bike ed5000. If you run out of battery on that, you just pedal it home.

Thanks dkw,  I did have to pedal home once.  A wire connection came loose and I didn't find it right away so I just pedaled home.  It took me 10 minutes instead of 4 or 5 minutes but I was happy to get home.

I should mention did have a near motorcycle version of this bike.  I have a matching front hub motor and a second controller that's progammable and I was running it at 80 volts.   It was a demon bike.  It would snap your head back and pop wheelies.  It was much faster than my 2010 DS although I was afraid to take it over 50 mph without any real suspension or disk brakes.  The fun part was I was able to commute to work 16 miles away on almost the same wh/mile so I didn't need a larger battery pack because I kept it under 30 mph the whole way (unless I was chanllenged) .  I could tell some stories but this isn't a bicycle forum.  

Sorry to hear that dkw.  I'm convinced the warmer temperatures are hard on these Agni motors.  Last week in the Bay Area here we had a day with 91 degree temps.  On that day I drove my zero with my cobbled together motor and measured the motor's outside surface temps and I got 150 degrees where normally I don't see much over 120.  So on these days I'm just going to take it easy.  The rest of the time I can race around more.

I had very good luck with seating the brushes.  I just drove the bike around town as easy as I could taking the slowest residential streets I could find.  That did the trick.  I do have one hill I have to climb to get to my house and that was where I think the burning smell was coming from initially during the break-in.   After that, the motor just got better and better with only a funny sound from the uneven commutator.

Zero has my bike now at one of their zero dealers.  They wanted to install the new motor for me which was nice of them.  I'm very appreciative of that  but while at the dealer I looked at some of new zeros for sale.  I test drove a 2011 S and man, I was surprised to see quite a number of improvements over 2010.  I thought '10 and '11 were pretty much the same bike but no, Zero was busy back then too.  The '11 has larger brakes, slightly larger battery, newer bodywork with a quieter ride, more indicator lights on the speedo, and, of course, that super quiet belt drive.  I wanted to take it home!  On the other hand, I should try a '12 (test drove one last January) or just wait for the 2013s to come out.  Hmmmm.

The drag of an O-Ring chain will lower the mileage. I'm willing to put up with more noise if it will get me farther on my battery. Also if I had to push a dead bike home, I wouldn't want the extra load of an O-Ring chain. In fact, using a "regular" chain, I carry pliers to remove the quick link, just in case I have to push the bike. Without any chain, I could also coast any (even slight) downhills I might come to on the way. These bikes roll pretty easily when not turning over the motor.

Trikester

I had to push my 2010 DS with a stock chain drive 5 city blocks and I found the bike very easy to Push.  It was somewhere between a bicycle and a heavier gas bike but closer to the bicycle.