The Manual Lever Position Sensor has been known to cause problems when it gets wet. It will make shifts much harder, and I guess could possibly make the OD light start flashing. This was a problem on the older E4OD trucks, and could be the cause of your problems. You might try to look into it. The MLPS is on the side of the transmission where the shift lever goes in. I would hate to tell you to replace it and then it not fix the problem, but that's where I would start investigating.