I know that the water pump has a different output from 98 to 99, But are they both outputs? I mean the coolant didnt output the pump one year, then the head the next?

What sled ???

The thermostat kit was installed in 99. It was an update for 98 if the sled had problems. There was a fitting tapped into the bottom of the head and also into the waterpump cover. A by-pass hose connected the two. There was also a spacer that fit on the head for the thermostat to sit. When the thermostat is closed, coolant takes the by-pass to heat the motor faster.

There was a change in the water pump inlet location also. The '98 had the inlet below the motor, the '99 had it coming into the top of the water pump. The '98 and '99 pumps used some different parts internally as well (seal in particular). Otherwise, they function the same and pump coolant in the same direction. As an FYI, it is possible to move the pump inlet from the '98 to the '99 location or vise versa.

thats what i was looking for thanks, whats involved in moving it

You need to buy the impeller cover, along with the gasket from a '99 and up motor and bolt it on. I think you might need one or 2 shorter bolts for the cover, as the old cover used a couple long bolts and the new cover uses all short ones. You'll need an elbow fitting for the bypass hose if you intend to use one. No mods are necessary. Whether or not you remove the old water inlet fitting is up to you. It is pressed into the water pump housing and sealed with an epoxy of some sort. The fitting can be cut off, or the epoxy bond can be broken with heat and the fitting pressed out. I like to remove the old fitting and press in a plug to make it look "factory", but that is personal preference.