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At this point I think we are. When I picked up the bike yesterday, my tach was completely disconnected, Now I'm going to have to put that back on, $300 later and my bike barely made it home. The part he did put on my bike I could have ordered from JP cycles and put it on myself. That was the part that was supposedly on back order for 3 weeks. I'm going to call a couple of shops that are about an hour away from me and pick their brains. If I get a better answer from one of them I will bum a trailer and haul it over. Coil or injectors?
? what are your thoughts? He at least narrowed it down to the front cylinder (but I could tell that before I even took it in) Too bad we don't live down the street from each other, we could get both bikes in the same building and fix them at the same time! We will outsmart these two bikes!
I think we we put our heads together, keep each other informed. Just maybe we'll figure out what the problem is with our rides.
Are we the only two with this problem???
Agreed... time to get someone else to look at it.
Changed my mind!!! I just called to see how it was going and he wasn't working on it. I'm bringing him home tonight! I'll give him a bath and a good polish and then I am calling another dealer for help. If I have to trailer him clear across Indiana to get him running right I will. Almost a month in the shop is way outta control.
According to the mechanic my plugs look good, their not fouled nor fuel soaked. He keeps saying electrical (coil or losing spark) I have a tach on mine too so he disconnected that to see if there was a connection problem there, no dice. I asked if there could be a problem with the plug wires themselves and he said that since there were two plugs per cylinder he could unplug one and it wouldn't hurt anything. Huh? I'm not a mechanic, but that doesn't make sense to me at all. I am ready to sign up for classes to become a certified kawasaki mechanic
then maybe I can take care of my own bike, and help you solve your problem 
besides not installing the FI2000, the only thing I haven't tried is taking off the hyper-charger. I disconnected the power commander didn't work. new throttle body helped but didn't really work, tried different maps on the power commander not much help there either. I'm waiting on a plug wrench to pull the plugs.I want to see what they look like. right now I can't even ride around the block.
I'm giving him until friday to figure it out. Then I will be bringing it home. It is drivable, just not for long runs. If it is not fixed I will be taking it to another dealer, maybe someone with more advanced equipment for finding the problem a little more accurately and in a timely fashion.
$$$$$$$$$$$$$$$ 
That sounds like the first time I took my bike in. Hope you have better luck
Still no bike
now he is saying it is something electrical, losing spark, in one of the cylinders. He still doesn't know what is wrong. sigh....... new fuel controler is on though.................more updates to come I'm sure 
three weeks is a long time. The last time mine was in the shop I had to have the throttle body replaced. It came all the way from Japan. Then they replaced my power commander unit. I had it back in less than two weeks then. Those new parts didn't help my bike run any better. Just cost me $1302.00, I don't go to that shop no more. Now mine runs worse than crap
I too am having withdrawals.
Anneoakley I have the same problem.. I did some checking and I found that the FI2000 makes your bike run richer, it doesn't make it run leaner. I have had the thought that my hyper-charger could be the problem but I can't change back to the old air system. because I didn't put the hyper-charger on. I was hoping you had found a fix when you put your bike in the shop. I haven't taken the plugs out of mine, I don't have the right plug wrench. Mine ran ok at most speeds until I plugged off the reeds to the smog control. Now it dies at all stopsand is hard to keep running at any speed.
1500/00 hyper-charger pro /FI2000 tri port roadhouse exhaust 2 into 1 look at wire connection from fi2000 to harness bad connection wires cut all most through had to cut add wire and hard wire still runs rich but so does 99 OME. cobra now has plug in leads that snap directly in to injector bodies (J+P CYCLES ) $199.99 wish i had this HOPE THIS HELLPS all-ways Cary extra plugs.
And there you have it!
Honestly, I don't know a lot about them. You could also ask your question here: http://forums.delphiforums.com/KawasakiDrifter/messages/?start=Start+Reading+%3E%3E You'd probably get a few more answers there.
Water in the hypercharger is a problem I've heard of before.
The FI2000 first generation (I have that) only has two pots. These things only ADD fuel, so the closer to zero, the leaner it is.
Try settings of 1-3/4 on pot 1 and 0 on pot 2.
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