I picked up a ct3. Seller said it was hard to start but he rode it. Honest bike lover. It feels rough when kicking. You can hear it. What should I do first pull the head and jug or the side case to look at the kick gear?

It'll be rusted growly main bearings--crank bearing. Likely the big end too. Especially if it's been sitting for a very long time.
Reminds me of my AT1--175, & had never been an issue then for no reason i can think off it wouldn't move freely after a reasonably long hibernation but growled on freeing up. Had to have rusted the mains although i never washed it before parking so shouldn't have been a chance of water ingress through air filter etc so i don't know. Oiled hell out of the mixture for a bit & came right & still ok but was the strangest think for no explainable reason.
Yours might be much worse than mine of course so up to you but likely a total dismantle & conrod kit plus main bearings. Or go oily in the mix & give it a bit more running. Full of joy for a Monday aren't i. Sorry Sir!!.

I'd pull ignition cover and plug and rotate flywheel by hand...  if it growls doing that then top end would be next.  Could be crank bearings as RT325 said. 

If quiet, then see if roughness happens when pushing kick starter by hand.  If only happens then, probably something in the kick start gears...  hopefully not the idler shaft/gear messed up from running dry that is end of trans output shaft. 

Thanks I’ll give that a try. Makes sense to take the kick out of the equation. I got a feeling the bearings ain’t happy.