Will a bad clutch affect all gears or can it affect shifting into one in particular?? From my understanding it would be the same for all gears.

It would be the same for all gears. shifting into one particular gear is most likely a synchro issue

Yah i figured it would be the same throughout, this issue seems to happen strictly for the 2nd gear and more so when it is cold out before the car has fully warmed up. DO you know if the synchro is covered by the powetrain warranty?

Thanks

Whether you are able to claim warranty varies drastically on a case by case basis. Some people are able to get their entire transmission replaced under warranty, while others have to pay thousands of dollars. Would suggest you switch the transmission fluid to redline and see if that helps. If not, then visit your local dealer.