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Flairs up, to the left of my right knee patella etc if I ride in Shimano xc mtb shoes and shimano SPDs.
What should I try/switch to? (Road/commute)
I find Shimano SPD's very restrictive. They have them on the spin bikes at the gym and the Q factor is wider than a normal bike so my feet want to flare out a degree or so more and I find that SPD's don't have much rotational 'float' before they pop out, so I find I have to force my feet into the right angle.
My Time's on my MTB have far more rotational and lateral 'float' meaning you can move your feet around much more before they pop out (I guess Crank Brothers will be the same or similar as they are a similar design). Obviously it means you have to rotate your foot a bit more to pop them out vs. SPD's, but you soon get used to that and it's never been a problem.
1 - get current pedals, shoes and position set up properly.
If above doesn't work,
2 -Repeat step one, but using Time pedals.
Flats?
Set them up properly, so there's equal float left and right.
Doesn't matter where your feet end up as long as you still have float either way.
http://www.cyclingweekly.co.uk/videos/bike-fit-and-maintenance/cleats-explained-how-to-set-them-up-correctly
Not a bad starting point.
Plus don't assume it's definitely down to the pedal/cleat thing. I get pain up the outside of my right calf edge/lower knee sometimes which turned out to be due to a muscle which stabilises the ankle. Pedalling seemed to exacerbate the issue, but it wasn't the root cause, running off road was. If changing cleat position/pedals doesn't sort things out, maybe see a sports physio next.
Shimano Road pedals work best for me. I could never get MTB cleats right, always felt a niggle somewhere. Road pedals, with wedges under 1 foot, have sorted this out.
Check your medial colateral ligament. Do you do any running. How tight are your hamstrings and glutes?
Change bikes, wait a minute...............