Knee Problems & Bike Setup

Doe's anyone have any good info / guide's on bike setup.

Earlier this year I bought a new frame and after doing Wildside & Karri Cup (and one XC club round where I totally bombed out) started to develop some inner knee issue's, to the point where even a 1-2hr XC ride was becoming painful. I've stopped my riding for the past 8weeks and have been receiving physio treatment for it, but my concern is I may have set this new bike up incorrectly (not really solving the problem). My physio has suggested to angle my heels in to allow load balancing between the muscles.

I've never had any issues with my previous bikes and am quite concerned that once I get back going again I'll be in the same position as now...

Any sugestions from the "Brain's Trust"
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I got the complete bike

I got the complete bike setup done at TBE Belmont and have not had any problems since. How do I know it works? Even if I raise my seat 20mm more than they worked out I am guaranteed to get a sore left knee. Done Karri Cup and Gibb River Challenge since.
Cost about $150 but worth every penny to not have pain.
Good riding
Mike.