Given where it hurts, your right knee sounds like some IT band irritation. The fact that you ride kneed in is further suggestive of that. Do you ride a triple? It could be a q factor issue. I had that in my right knee, too, when I rode a triple. Now I ride a compact for that very reason.
As for you left knee and left sitbone, did your fitter suggest that your left leg is shorter than your right? The pain you're experiencing on your left side suggests to me that your saddle is too high for your left leg. If your fitter concurs, then you might try a shim in your shoe or under your left cleat. Otherwise, drop the saddle down a smidge, depending on the leg length discrepancy. You set saddle height for your shorter leg.
I know little about achilles issues so I have no suggestions there.
If your fitting covered future adjustments, I'd go back and talk to your fitter about these issues.
Live with intention. Walk to the edge. Listen hard. Practice wellness. Play with abandon. Laugh. Choose with no regret. Continue to learn. Appreciate your friends. Do what you love. Live as if this is all there is.
--Mary Anne Radmacher