The valving is different. You won't really notice it though unless you do hard braking.

 

So if I put the axle from the 99 in the 06, it will be fine? Do you know if the u joints and all are the same?

 

Should be. The only difference on the housing is the way the flanges that the brakes bolt up are clocked differently. They changed the casting in the center but all the axles bearings and seal are the same with the exception of the yoke. I guess there was some sort of seal change on the front pinion in 04 You have to use the correct seal with the correct yoke. Other wise the joint should be the same.