Are you using a walking foot? That always helps me. Also, make sure you have as big of a space as you can manage. Lay most of the quilt on the table to keep the weight off you. Other than that, just a warm soak in the tub afterwards. I've quilted large bed quilts on a portable machine and for several days afterward the arms, shoulders, back, neck, etc ached. When you're done and aching the satisfaction of being done will lessen the pain.