I say the engine had low power output when you serviced it, am I correct? Now then you get the timing set and she runs good, and now producing more horsepower and torque. This now puts an added strain on the transmission. My point is, the transmission was probably already weak, and now that the car is running at it's peak, the transmission is showing signs of failure. There is no possible way for you to damage the transmission by replacing timing components, alternator and waterpump...