Fit matching between bikes - problems just above kneecap towards inside on gravel bike

Hi fit gurus -

A few months ago, I set up a new to me gravel bike with the goal of matching my road fit by first prioritizing the saddle height and setback to have the same saddle position relative to the crank center. My basic understanding is that this is where I should anchor things between the bikes, and then adjust stack and reach as needed to fully match. The reach is roughly comparable to my road bike, but there is less drop to the bars vs. saddle as it’s currently setup - which I thought would be a safer starting point.

I’ve ridden it a few times without issue, but the last ride I did was > 4 hours, 60 miles and I got a lot of soreness just above my right knee, towards the inside of the leg. Feels like a ligament or small muscle that comes diagonally from center of thigh to inside of leg in that area, angling down the leg, if that makes sense. Was sore for about a day and a half, and then went away. Never felt this on my road or TT bikes. For what it’s worth, I have spent more time riding TT than anything else this year - e.g. lots of time rotated forward / low front end.

What aspect of the gravel bike fit would you suspect to cause this? And in the absence of another stem on hand, would you make a saddle adjustment up or down to mitigate it? Or would dropping the bars to more closely match my road bike (and a bit more like my TT riding) be expected to relieve this issue?

Thanks for any advice as I’m hoping to get out for another big ride soon on it!

If your gravel bike is like mine its got way shorter cranks than the road bikes. Try taking the dimension from the pedal axle at the bottom of your stroke so your leg extension on each is approximately the same.

yes this is what I would suggest from that point of view, also are the shoes the same for both? If not that can easily cause this sort of problem. Particularly if the insoles are not the same this leads to knee tracking problems (due to proprioception) and will often manifest in this sort of pain/ issue.

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Very good point - forgot to mention but I did consider that as well, and they are both 172.5 mm.

Yes - I’m actually using my same road shoes and insoles - I move my Assioma power pedals over to it when I ride it. (it’s pretty easy gravel - well maintained dirt roads)