I have a 2006 2wd rancher and looking to put 25" mud runners on the back and maybe the front.

WOrried about losing power? also could I upgrade the back to mud runners and leave the stock cl's on the front in the short term? They are 24"

 

I'd put the same size all round. Now as for power just add a K&N power filter and you'll be fine. I've got a Rancher 350 4x4 with 26" mud runners with the power filter and no problem.