I am glad you got it all figured out.
I had a simular issue with the left shock during my Pro Action rear shock installation. Below is what I mentioned about it in my original rite up about the installation.
(QUOTE) #3 from my original posting below concerning shock length.
#3 The right side shock went on easy and threaded right on to the shock mounting brackets top and bottom.
The left shock did not. I had to put a little pressure down ward on the swingarm by placing a padded short bar or long screwdriver between the frame and bottom shock bracket and pull down a little to get the shock bolt straight so it would thread into the lower shock bracket. (I think this was because the drive belt held a little upward tension on the left side). It did not take much effort at all for the bolt to line up. (END QUOTE)
After it's all said and done it sure feels good. Now go ride the heck out of it.
You can now fine tune your shock click adjusters to your liking. I would adjust 1 click and ride a long ride. Then adjust (softer or harder) for me softer and try again. It took me about 4 rides to get it all dialed in perfect for our set up. I settled on 2 clicks out and also liked 3. Of course this adjustment will be diffrent for everyone.
Our shocks came set at 5 clicks. Pro Action says most find somewhere between 3 & 6 clicks to work for them.
Ride Safe,
Bill G