SPECTRE drive shaft issues...Please help

Does anyone have any experience with lowering a shaft driven bike? I need any info I can get because I cant find much online about the shaft driven bikes.
Does the shaft have to be level?

The reason I ask is because I have a shaft driven bike that is lowered quite a bit with rigid struts instead of the original springs. When you roll the bike, no matter what gear, with the engine off, you get a clunking sound that comes from the rear casing of the transmission where the drive shaft connects to the engine/trans assembly. I'm assuming that the shaft is at a slightly upward angle and is binding somehow. Is there anyway to fix this problem WITHOUT getting longer struts and raising the bike? Has anyone ever run into this problem lowering a shaft driven bike?

If possible find the forum member "Zoro" he has a ST with a shaft drive. He might have advice..

Loosen the clamps at the boot, and slide it back to expose the shaft coupling. You may see where the noise is coming from. Or you may have to remove the rear wheel and shaft housing. Somewhere you would most likely see worn joints or if the angle is to much, the Knuckles hitting each other. Operating angles of universal joints normally don't exceed 3 degrees max. Any more and they are generally a high failure Item. That's the standard U-joint cross. Have you ever pulled it and lubed it like explained in the service manual? That's the Bikes shaft, OK?