Answering a few questions...
--I ride a hybrid bike with flat bars and upright geometry. I have smooth, skinny tires (Schwalbe Marathon).
--Now that you mention it, maybe my seat is too low! I'll mess around with that over my weekend.
--The pain I'm feeling is DOMS, not joint pain.
--The hills are gradual, but the ride home is pretty much a constant climb. I'm not sure how much downhill I have on the way home, but I do know that it can be measured in yards rather than blocks or miles.
--I stretch, hydrate, and eat like a horse. My diet is mostly healthy, except for when my wonderful coworkers bring me fast food.
--I have two panniers with a combined weight of about 7-10lbs. (depending on weather - big temperature change = pack more layers).