I always use tapered wooden shims, the type contractors use to shim windows & door frames, and drive one into the gap where the disc usually fits, then remove it. It's an easy and non-damaging way to drive the pistons back into the caliper and provide more clearance. Just remember to tap the brake pedal or lever to push the pads back to their normal position before riding!
I learned long ago that the easiest way for me to remove/reinstall the rear wheel was to remove the right saddlebag lid and body. With that gone, you can SEE everything! At least for me, it adds about 25-min to the job.