I just got a new bike, too. And I think I test rode the Felt you decided on. ( It was very, very nice! ) The previous Sunday I went 50 miles around town, and did a very similar 50 mi on the new one this past Sunday to compare. My left knee was in pretty bad pain after a couple hours in the saddle, and all of the next day. I did a lot of climbing, but not 7,540 feet worth.
Two Clydes on new bikes, both with knee issues that didn't come up on the old bikes, makes me think fit is what's going on. I'm pretty sure that's what's going on with me, anyway, and you seem to have the same story.