Leaking water pump - transmisson failure

Make Toyata
Model 4Runner
Year 2000
Engine Size 3.4L - 6 Cylinders
Seating Capacity 5 Seats
Fuel Type Gasoline
~ 55,000 Miles

I think my SUV was misdiagnosed. Let me explain.

I was driving the other day and the SUV overheated. I stopped and had the SUV towed to an independent mechanic who had previously worked on the SUV. The independent mechanic said the radiotor was filled with a "strawberry milkshake" liquid and the radiator was probably clogged and needed to replaced. He also replaced the water pump and timing belt. He then flushed out the transmission fluid and coolant.

About, 4months or 4,000 miles earlier the same mechanic said the water pump was fine. I initially took the SUV to the dealer and he said the water pump had a small leak (by visual inspection) and that the pump had to be replaced. I wanted a second opinion so I took the SUV to the independent mechanic and told him to check the water pump and that is when he said the water pump was fine.

I am wondering if the overheating resulted from a water pump that was leaking or some other cause. I believe the overheating resulted from a water pump that was leaking and led to the tranmission cooler (which is in the radiator for this model) to malfunction causing the coolant to leak into the transmission.

The independent mechanic says that the head gasket is fine so the water pump was not leaking. He is saying if the water pump was leaking and the SUV overheated the first thing that would go is the head gasket.

Eventhough the head gasket is fine can a SUV that is overheating lead to failure of the radiator and transmission cooler. Resulting in coolant getting into the transmission. The Int. Sprag was faulty and 2nd gear was not working the transmission guy had to rebuild the whole transmission at a cost of $1,800.

I feel the independent mechanic did not recognise the water pump was slowly leaking and he did not give me a good recommendation.

Thank you for your response.