I know this isn't specifically a commuting question, but I don't know what forum is more appropriate. I've noticed over the past couple of weeks (maybe since I went clipless) some pain on the insides of my knees. I rarely mash (my RPM is usually between 90-100), and I'm just wondering if it might be a fit issue.

I read that I can try moving the cleats on my shoes further to the outside, which I've just adjusted, but haven't ridden this way yet. I'm just wondering if there are any other specific fit issues I should look at. I have my seat all the way back because otherwise I am not sitting on my sit bones (still feels too short at times), and I've been thinking about raising my handlebars a little to move my weight back. Is this hard? Do I need any special tools? Sorry, don't know very much about bike mechanics.