Shimano custom fit R300 road shoes. I'd purchases the M300 the previous summer and loved them. The vacuum formed fit is so good you barely feel the need to tighten the straps. Although the transition into the mountain shoe was smooth, I couldn't say the same of the road shoe. Almost immediately I began getting some weird tendon strain that I'd never felt before. Initially I thought it was saddle height related. Then cleat rotation and finally it could have just been that my 10 year old Sidi's were so clapped out that the switch to a new stiff carbon sole was just too much.
The discomfort was never unbearable and it never got worse, even after multiple century days. On the mountain bike my knees were fine with no discomfort at all. First I messed a very little bit with my saddle height. I checked my fore-aft and cleat rotation, all was well. Next I tried some pedal washers to increase my Q factor. I figured this was it for sure as Q factors have been decreasing on road bikes but are still fairly wide on mountain bikes. No luck.
Enter the lads a bikefit.com. Sitting at the shop mid-summer a small clear package arrived with what looked like a orange half insole inside. The small wedge was thinner on one side, thicker on the other. It's known as a varus wedge. After going through SICI a few years back I've always steered folks away from wedging because it would be really easy to mess someone up. But I'd be the perfect guinea pig for myself.
I sat on the thought that this could be the answer so when I came upon the Bike Fit booth at Innertbike I thought I'd have the pros give a look. They pulled out their FFMD and gave me a measure. Not to my surprise the Fore Foot Measuring Device said my left foot (the issue) had a 12 degree varus cant, my right, a 6 degree. They suggested two 1.5 degree wedges on my left, one my right, handed me a set of in the shoe (ITS) wedges and I was on may way.
After running the "in shoe" version which only allowed me to run one, due to shoe volume I decided to order up the yellow cleat wedges along with a set of longer cleat bolts. After riding these for a couple weeks now including some power intervals on the trainer it seems to have worked. Typically those big gear sessions would aggravate it. So if you got a tweaked knee you might want to give this stuff a look, but adjust with caution, it'd be pretty easy to make it worse.