if my crank pully is at 12 oclock position and the dowel on my cam is at 12 oclock is it possible for my cam timing to be off. i replaced my timing chain and guides and matched to shiny links to the dimples on both gears. now it is running rough. was thinking maybe while putting everything back together maybe it skipped a tooth.

 

Were the cam and crank sprocket checked for minimum diameter? These will vary the valve timing

 

no i did not check that both the cam gear and the crank gear were new and came with the timing cover kit.

 

Probably not an issue, but in the future it's best practice inspect new parts meet the requirements. Errors in manufacturing do happen, people do out incorrect parts back into packaging and return them, and chainstore parts counter people are no better than fast-food emploies in a lot of cases.