The 'clicking' part is the same as when you have the kickstarter held off of the stop when the engine is running. So, I think you may have the kickstarter out of position when it is at rest. I don't have a 500/550 manual for you to refer to, but most bikes are the same in this area: there is a certain spot of rotation for the kickstart gear when it is installed. This is its 'neutral' spot, so to speak, where the ratchet is not engaged. Then, when the arm is pulled down a little, the ratchet pawl (aka finger) slides out to engage the ratchet teeth.
If the ratchet pawl is engaged, the engine's shafts cannot be turned backward, because the gears will all stop against the pawl. So, you need to go into the ratchet and see if you can discover the neutral spot, and why you are not there now. It's probably just sitting on the wrong spline on the shaft.