Can overheating after replacing water pump&timing belt

Honda civic 2000 DX hatchback. Mileage 101,000. I recently had the timing belt and water pump replaced. Unfortunately the water pump was defective (so I was told by the mechanic) and after I picked up my car from the mechanic the car overheated while I was on the highway. The thermometer went all the way to the top and I did not realize. I only realized when I saw smoke coming out of the hood. I stopped the car, towed it to the mechanic and since then they replaced the radiator, flushed & checked the cooling system (funs, fluid, etc), replaced the thermostat and anything else they thought was necessary. Since then my car is overheating in a random fashion. The thermometer sometimes goes up to 3/4 high while driving (both in the highway going 50-60 mph or in traffic). When it goes so high it usually comes down pretty quickly. Other times it remains above the middle for a while.
I took it back to the same shop several times. However, they could not figure out anything wrong with it. I plan to take it to another shop but I wanted to ask what else might be causing this problem. Before the water pump incident my car was running perfectly. Is it possible that the initial overheating caused motor damage (or any other damage) to the point where it can't be fixed completely?