I have no doubt that quad-pull you  mentioned is still there, at least residually. Quad imbalance is a major  cause of knee pain, and can lead to actual knee damage if left  unchecked. More disturbing is the ongoing problem with your ankles. Does  your footstrike involve over-pronation? Are you wearing motion control shoes that may be stiffening your footstrike?  Does your job require a lot of standing, or a lot of sitting? Standing  may be great for your quads, but too little rest for your ankles. On the  other hand, sitting may be a great way to rest the ankles, but  stretching your quads for too long.

My advice  would be to foam-roll or massage out those quads (pressure from above  knee toward hip), paying special attention to the tightest and most  painful spots that may be perpetuating the imbalanced pull on your  knees. If the ankles become extremely warm with use, there is likely to  still be some inflammation in them. There are no muscles in the ankles  to create this heat, so increased blood flow must be there for some  other reason. One useful strategy involving ice, has been to apply ice  to the ankle long enough to dull the pain, and take advantage of that  opportunity to move the ankle through its range of motion to restore  healing circulation while painful swelling is still suppressed by the  ice (or cold pack). One recommended exercise is to trace the alphabet  with your toes, but you want to explore range beyond this point.

Most  importantly, you need to find out the reason behind the stress on both  your ankles and quads. It can involve anything from foot/arch structural  issues through problems with the structure and muscle tone of your hip  and back. A desk job would be a definite strike against the health of  your hips, unless you are able to move around frequently. It is  unfortunate that you have ankle problems in conjunction with the other  potential problems, but there is a way to help address these problems  without undue wear and tear: Try pool running, the no-impact strategy  for rehabilitation... http://www.active.com/running/Articles/Pool_running_can_be_a_real_workout_and_great_recovery_exercise.htm

If you have the average desk you may need the "modesty panel" removed so   you can prop your legs up for at least part of the day. I'd stick with   the no-impact training until your ankles can get ahead of the wear and   tear. Make sure you are getting adequate sleep, plenty of vitamin c,  as  few refined foods as possible, and no food within 4 hours of bed  time. Try a small thin pad (quarter-dollar sized) under the ball of your  foot (under the insole) before you switch to motion control shoes,  which may make things worse by limiting shock-absorption. The pad can  correct the knee and ankle symptoms over time by modifying your need to  pronate.