Finally got the tools I need from ZDMak, they have quite a big selections and the price is very reasonable. The water pump replacement project was easier than I expected. The brown stuff I posted in a picture previously are rust that came from the water pump pulley. I guess the coolant leaked from the weep hole and falls right down to the inside surface of the pulley and cause it to rust.
Also I found that the fine particles inside the cooling (making it turbid) are attracted by a magnet. After the water pump was removed, the timing case has some grind marks on it, looks like the turbine thing on the inside of the water pump is grinding the timing cover. The pump axle feels a little wobbly compared to the new pump at hand, not sure why it would grind the timing cover but it did. Anyway, I spent the most time trying to flush out the dirty coolant, the actual water pump replacement probably took me about 2.5 hours. The truck is running fine and smooth now and no leaks. I think I will take it to the dealer and have them flush out the coolant one more time. Anyway, our truck is few months short of 8 years and only have 66k miles. It seems a little early to have a failed/failing water pump. I took some pictures of the damage components, if anyone is interested.