I don't recommend doing a flush. Just a drain and refill. Flushing can cause issues for higher mileage transmissions. Your transmission is way past due for a drain and refill. It should be done every 40k-50k miles and the PTU (if you have AWD) needs to be drained and refilled every 30k miles. The PTUs contain very little fluid and it is baked by the exhaust, engine and transmission heat. This requires that they are serviced every 30k miles. Also, don't follow Ford's service recommendations for fluids. Their recommendations are far too long and will not allow you to get the most longevity from the engine, transmission, PTU, differential etc. The engine oil and filter should be changed every 5k miles at a minimum. The differential oil every 100k miles. The brake and power steering fluids flushed every 80k miles. Coolant every 100k miles. Doing this will go a long way in getting the most trouble free miles form your drive train.
Also, if you have a V6 engine keep a close eye on your coolant level. These engines tend to have the water pumps go bad and this can result in catastrophic failure of the engine. This is due to the water pump being an internal design and when it fails can send the coolant into the oil very quickly. Any, and I mean ANY, drop in coolant level is cause for immediate concern. The reason for the drop needs to be determined ASAP. In fact, I don't even recommend driving it to a shop and instead recommend having it towed there for them to check out where the coolant leak is occurring. The 3.5L/3.7L engines are darn near bullet proof otherwise with good maintenance applied to them.
Lastly, I only recommend using Ford Motorcraft brand fluids. They are specifically made for your vehicle. Off brands are not necessarily formulated to meet OEM requirements.