my exracer had si issues and i found long lining him much better than lunging when we started rehab. Did long lining for a few weeks, and started gradually bringing in poles etc. Also did a lot of inhand work gently moving him over poles and turns. Eventually lunging was great, very important to watch the surface you are lunging on though. the yard i was in had a very deep sand arena, so it wasn't suitable when it got too deep.
At the start my lad kept dragging a toe when ridden, but eventually he stopped once he had more muscle built up. It was really building up the muscle and topline that helped him the most in his recovery.