I bought a "backup" bike at the same LBS that fit me on my "good" road bike. We swapped out stem, saddle, handlebars and did a lot of work to match the fit. The geometry was very similar between the two bikes to begin with. I left my good bike with the shop so they could compare the two side-by-side doing the setup.
And I still could not ride the new bike more than a few blocks without having severe knee pain.
I had dual campus:SPD pedals on the new bike, MTB SPD pedals on the good bike. So I got the same brand of MTB SPD pedals installed; that solved my knee problems.
It is amazing how locked into a certain fit and bike frame/components you can be after thousands of miles on one bike.
I feel like I could have been in the story "The Princess and The Pea".