I say, get some regular green antifreeze and fill your car with it... just to see if the car overheats after a few weeks...this way you can easily determine if the straight water in the system is causing the issue.if it does not overheat, then flush the green stuff and get some prestone universal (yellow) coolant in there to avoid future damage... If it still overheats, move to water pump and inspect/replace it.
a few more tips
Make sure you do not have an air lock in your cooling system, that can easily cause an overheating issue. Im not sure about the 3.5l but the 3.8l has a few air purge valves you are supposed to open after a radiator flush.
make sure your fans are operational, i had one dead fan in my 98' and if i sat for more than a few minutes on a hot day the temp would rise above the 3/4 mark towards the red until i got moving again on the road...