In case you are still wondering, there is a hole on the back of the water pump flange that can be aligned with the Ridge on the top of the water pump.
Align the hole just to the driver side of that Ridge and place the tool (there is actually a tool made for this; I used another tool and also think one could be made. Once you have it aligned you will see how it works and what will work to hold it in place.)
When you turn the bolt the tool that you use will act as a stop on that ridge.
When you put it back together just align the hole on the passenger side and it locks it as you tighten the bolt.
If I was home I would get pictures of it for you but I just did this job about 4 times on my 99 (don't ask!).
As previously posted, unbolt the 4 tens holding the upper rad support as this allows just enough room b/t the rad and clutch fan bolt