Added Aero Bars, Should I Adjust Seat/Stem?

I added some aero bars to my Trek 5200 a few weeks ago. They really do help
me to ride in a more aero dynamic position for longer times. I'm about 1.5
MPH faster too :-)
However, after riding about 20%-40% of the distance (usually ~40 miles) in
the bars, my legs feel stressed behind the back of the knees and sometimes
below the knee caps. I know better than to ignore these clues.

Do I have to re-adjust the seat or stem now that I'm riding in a new
position?