Mod,
I have had a horrid time trying to clutch my SC Nytro ever since I got it. I have tried just about every clutch setup available and nothing works. Always the same results pulls good for a couple climbs then the clutches get hot and I lose all my track speed. This spring after I got done riding I started really looking everything over and discovered what you are describing. In a ddition to the space between my clutches being out of spec (to short) they were not parallel at all!!! First I pulled some shims to get the offset right , then putting a clutch alignment tool on it the front of the secondary would touch and the rear was probably 3/16 of an inch from touching. (never measured). In addition, as I mentioned above, the center to center alignment was shorter than spec by about 1/8 of an inch as well. There are no gaurantees this will fix my clutch issue, but I am hopeful. Being that far from parallel puts a lot of strain on the belt and has got to create a ton of heat. Also, being to close together would likely mess with the clutches ability to keep the belt tight.
Now, as for how to fix it.... FIRST, Buy a clutch alignment tool from ulmer racing. It is by far the best quality one I have ever seen. It is machined so you don't get the poor cut quality like you do with the cheap water cut steel ones. Alan's is top notch. I used both styles as a double check since I had them both and the cheap one is a little easier to fit in place for offset measurement.
Once you establish exactly where you are off (center to center and/or alignment) loosen the long motor mount bolt in rear. You do NOT have to remove it just losen a few turns. Then remove the nut from both of the front motor mount bolts. You do NOT need to remove the bolt just the nut. Now you need either the yamaha motor mount tool or make your own. You can make your own using a deep socket that you grind so there are two teeth on it or weld a key way on the end of a shaft. You need to turn the front motor mounts to move the motor. As you do this you can make it go forward, backward, left, or right. For example I needed to move my motor forward and twist it in a clockwise direction looking at the motor from above. I did this by turning the left side out and the right in.
When you are done adjusting tighten the REAR mount first and re-check alignment. Then tighten the fronts and check again.
I was amazed that I had to move the front of my motor over by probably 3/8 or more of an inch to get proper alignment. Something may be bent in my frame I am not sure, I will look into it more this fall, but at least now I know my alignment is correct.