Pain in right knee only

[Blueberry]

Is your saddle position the same front/back as your old bike?

CA

[Running Mommy]

Find an lbs that has a GOOD fit person. A certified fit person and make an appt. Nine times out of ten something like this is is due to a bike fit problem. Something somewhere needs to be adjusted. But you really need a professional to look at you. It's very hard to do it yourself.
A good friend of ours recently made an appt with our fitter because knee issues had cropped up. He's an accomplished cyclist and Ironman. Recently his frame had to be replaced due to warranty. Even though the bike measurements were taken, documented, and the new frame was set up to the original specs, he felt that something was wrong. So he decided to start moving things, and he only made a bad problem worse.
Turns out the new frame has a different seatpost set up, and that was enough to throw things off.
Our fitter found a couple of key issues and addressed them, but because his knee is so angry (he waited too long) he is going into lake placid this weekend injured. So in other words- address the issue sooner rather than later!
Good luck! I'm sure with a good fit person they will have you pain free in no time.