First, "normal" water won't hurt anything in the short run. Distilled is best, but if you have a water softener or municipal system that's softened, it's pretty close. Where you run into trouble are with waters having a high mineral content.
How many miles? and are you using any coolant? If so, how much and how often?
The reason I ask [and from your description] is that the '99 model 4.0 used an inferior head casting, which cracks at about the 90k mark, if not before. This head (the part just under the valve cover) is labeled "0331" on the driver's side of the engine, behind all the intake and exhaust.
If you have the 0331 head, and are above 90k, are losing coolant and can't find the leak, you've probably got the hairline cracks that allow coolant to escape when it gets hot. The head will need to be replaced; I'd also change your oil every 2k until you get the new head, as coolant in your oil will wear the engine much faster.