icyclist 

"I notice with my regular road bike i get the same result with clipless pedals. Same soreness etc. Im wondering if that isnt my issue."

And your knees - do they hurt, too, when you ride your road bike?


"i ran a 48x17 all last season"

What was this season? You mean last year?


"starting getting some knee pain and soreness. "

Was there some time interval when you didn't ride?


While getting a pro fitting would be great, it's not something most people and do, and most people seem fairly comfortable on their bikes. And if you've been riding all along without problems until recently, with pain only now showing up, then try to figure out what you're doing differently from before.

My first and probably only guess, based on the assumption you stopped riding for a while, is that you're simply overdoing it - as in "ll pound out 24 - 35 miles in a ride....maybe it is just from over use?" - yeah, it could be you're simply overdoing it. What happens when you ride easy? If you feel fine, then ride easy for a while and gradually increase how hard you push yourself.

And/or use a smaller cog for a while. There's a reason a lot of stock bikes come with 42x16 gearing, and not with gears that are a lot higher or lower. 42x16 is a good starting point for most people. If you've taken some time off, you might just need to build yourself back up to your taller gears.