Today I...

First off I'm going to lower my saddle a bit ( I think It's at the right height at the moment though) ride with that for a little while. Then maybe fit pedals and straps again to see if that helps.

I used to think my saddle was a good height, too, and if anything I kept trying to raise it to alleviate knee pain - it turned out that I needed the saddle much further forward than the seatpost would allow, and of course lowering it will move it forward a bit due to the angle of the seatpost and tube. I then looked at photos of the bike from years before, when I rode it extensively with zero knee trouble, and the saddle was so, so low - I couldn't believe it. I put it back like that and at first it felt silly and that my legs weren't getting a good stroke on the pedals, but I got used to it and sure enough my knees were fine.

I later noticed that the bike in question was very "long" (as touring bikes tend to be), had a long top tube and the top of the seat tube was a long way back from the BB, so probably what I needed was a tighter frame geometry as well.

Knee discomfort definitely isn't something to "ride through" - $hit will fuck you up, now or later in life.