Grizz,
the simple answer is if you have a problem it's always going to be a problem! You can help yourself though,get a chair that you can mount your controls to so you dont have to reach.
Most computer/office chairs have padded arms,remove the pads and attach some shelves/platforms to the arms to mount your stick and throttle to so you can sit back and opperate the controls. If you use pedals,mount them to a piece of plywood and make a couple of holes that you can place the chair wheels into,then you wont chase the pedals around!
Mntman made a nice setup that mounted to his chair,I think it could easily be removed if needed also! If you search the help and training forum I think you can find a pic or two of how he did his.
Having a chronic ...pain condition I understand what you're going through!