What can I do to eliminate knee pain while riding

Okay - so.. typically when I ride it's during a lesson, show, or clinic and I'm in the saddle for an hour at the very least. Lupus runs in my family and I've already got symptoms of it + rheumatoid arthritis. After riding for an extended period of time, I start to have knee pain - mostly in my right knee. I've tried jointed stirrups and ironically they caused MORE pain than they relieved. I've thought about trying the Bow Balance stirrups but I'm afraid it'll be the same thing. I have "conformational issues," as my trainer likes to put it, because I've got a 33" inseam but I'm only 5'4". This makes it hard for me to fit really nicely in a saddle without my leg looking too long (even if my stirrups are at the right level).

I know I have a problem of turning my toes out when I jump, so could this be part of the reason for my knee pain? Could it be the fact that my legs are so long? Does anyone else have this same problem and if so - what have you done that has actually worked?

First off, are you sure this isn't related to the RA. Are you on anti-inflammatories or steroids etc. If you are suspecting you have lupus, they can do a simple blood test, but you probably already know that.

So start there first, see if there is actually something CAUSING your knee pain vs a conformational issue.

Are you riding english then? Sorry not familiar with Bow Balance stirrups. I know that my mom had really bad knee pain that was cured when she went to the things that actually turn the stirrups the correct way. I can't remember the name of them.