I agree morning aches/pains are not just part of aging.
Great to hear you have a history of being active and are continuing to be active.
Addressing the impact of long periods of sitting will definitely help.
At night undoing the impact of the day and/or proactively addressing something in the morning: Quads, psoas, hips, t-spine or wherever needs attention.
Taking a look at your sitting position can help too.
The Stability Problems With Sitting
Episode 276: MobilityWod Google Talk: Desk Bound
May or may not be possible to make changes to your set up, however, things to keep in mind.
There are several episodes in the archive which address sitting position.
One to get started
Episode 251: High Skilled Sitting/Abdominal Bracing
Another option for down regulation is Kelly’s Down Regulation Class or there are down regulation from the archive.