I had the same problem but this was prior to going clipless and I was riding with toe straps, so I knew cleat angle was not the problem. Not saying that this is not the case with you but there are other things that may have contributed to the pain.
Your post starts with "While I have been mostly doing shorter off-road XC riding, I have done a couple of road based longer rides for charity."
My guess here is that your XC may mean you spent longer in the smaller/mid ring and you spun more but switching to longer Charity rides which may have been on road necessitated use of the big ring for far longer periods which meant grinding instead of spinning thereby increasing the load to your knee. This is of course just a guess based on the above sentence.
Although I ride a road bike mine was actually changing cycle clubs upping the pace and spending a lot longer in the larger chainring than I used to thereby increasing load to my knees.
By staying away from the big ring for a bit upping my spinning rate rather than switching to the big ring the pain went naturally. I am not saying that I never ever use the big ring but on a road bike anything up to 19-20mph can be achieved in the smaller of the double rings. I change up now with a bit more thought and concentrate more on increasing RPM (to the point of my natural ability) prior to changing up. The pain comes back if I do too much too soon so please bear the above in mind together with seat height (too high or low can cause havoc), cleat position and angle and upping mileage quickly and substantially.
I can only relate your pain to my previous experience and the reason may not be the same but exhaust all of the points on here rather than just pinpointing one and you should get there.
Good luck
what really needed to adjust was the laterall movement of the cleat.
