What mileage do you have on that tranny?
At higher miles it would NOT be adviseable to do a complete flush. This would only cause your tranny to shift worse, and grind possibly more (if it grinds at all, yet)
If you are pushing over 65-70 thousand miles, I would suggest doing to drain plug method, and refilling with approx. 2Qts of fluid.. Do this once every two weeks until you get clean fluid out.
Ray