I also had to replace my water pump. I had the coolant flushed and refilled at the same time. If your temp light is flashing it means you have a low coolant level. I suggest you have the coolant flushed and refilled. It is a tricky job but well worth the peace of mind.
Here is an article on replacing the coolant tank. Scroll down to the end and it gives a good explanation on how to bleed the coolant system to get the air out.
Linear Mode
