Take it from a dealer.... contacting Mathews directly will only get you pointed to your nearest dealer. Thats kind of the idea after all.
The clicking you are hearing is coming from the yoke bushings. That is, the plastic pieces over the end of your idler (top) axle.
What you need to do is press the bow and remove those bushings. Take a very light greese (we use Penn Muscle Grease, designed for Penn Fishing Reels at our shop) and lightly coat the inside of both of those yoke bushings. Your click will go away. I don't know exactly what causes it, but I do know that fixes it 100% of the time in my experience (this assuming we are talking about the same issue).
With your limb turrets... historically there are two sets of limb/pivot combinations with slim limb bows... there are 1s and 2s. You will know which you have by the number of dimples on your limb pockets. doesn't matter which you have, BUT your limbs and your pockets MUST match. If your dealer flipped them, (I am assuming he knows what he is doing) then he might have swapped the wrong one or something.
Not entirely sure I understand your situation... is there a slight pop or rub on your cable as it comes into the valley? There was an issue with a few 09 Drenalins and Reezens that did this. Only option for a fix was to replace the limbs and pockets... 100% covered under warranty.
If you do call Mathews... and if they entertain you... speak to Bob in the warranty department... super nice guy and a freakin' genius when it comes to the bows he works on. Whatever issue, concern or noise you might have... he has seen it all, heard it all and knows how to fix it all.
One way or another, you'll get taken care of.