Given your overuse and knee issues, I think you should concentrate on spinning, but based on your OP, I wonder if you might be choosing too easy of a gear. When you say you were using your "easiest" of gears, do you mean that you were using your 26-32 or 26-34 gear? On what you describe as "gentle inclines"? If so, I'd suggest that those gears are perhaps a little to easy for that terrain. It's no wonder that you didn't like how little resistance you had. Remember thay your bike's gearing is intended for loaded touring.
To me, spinning up a hill does not mean that my cadence doesn't slow down from my usual flatlands cadence. One suggestion I read is that you should aim for a cadence that's 75% of your usual. In your case, I might bump that up a bit to protect your knees, but it is okay to slow your cadence down a bit. Just try to avoid being in a gear that requires you to push or grind your way to the top (unless that's the only way to get to the top, like in Brown County).
Certainly, if you feel any twinge in your knees, shift to an easier gear. You might want to try some hill repeats, too. Pick a moderate climb and experiment with different gears, paces, and cadences. What feels "good" to you?
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