so many questions!

Originally Posted by
OakLeaf
Where in your knee is the pain?
Did your seatpost actually slip to where your seat height was lower than you normally set it?
Are the crankarms on your new bike the same length as on your old bike?
Get a torque wrench for your seatpost clamp bolt...
The knee pain is on the bottom of the front of the knee cap. Although, while I was commuting to work this morning, there also seemed to be pain in the back of my knee. It was absolved within hours of waking and putting on my running shoes. I know that my right leg is dominant and that I have to make a conscious effort not to let it do more work than the left leg.
Yes, my seatpost actually slipped down....I'm in the process of getting a torque wrench 
Yes, the crankarms are the same length 

Originally Posted by
indysteel
What kind of crank do you have on your new bike--a triple, standard double or compact? What kind do you have on your old bike? How sure are you that your saddle is at the correct height? Do you have a leg length discrepancy?

Originally Posted by
CA_in_NC
Is your saddle position the same front/back as your old bike?
CA
It's not at the same position on the seatpost itself, no (the tick marks don't line up).

Originally Posted by
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.
Ugh. I thought you would say this.
Unfortunately, I am wary to spend additional funds on a fit right now... Nonetheless, I have had a difficult time finding a good fitter for a long time. The one I had in mind moved to another city last winter. The one I had been to was not as meticulous as I would have liked and never followed up. Also, it is rather far away for a fitting that does not meet my expectations 
::sigh::
I will keep my eyes open for a good fitting and will plan on getting a fitting.
Ana
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2009 Lynskey R230
Trek Mountain Track 850