Are the 99 5.3 and th 05 6.0 intake manifolds the same besides the trottle body?

 

The 99 will probably have the fitting up by the throttle body for the EGR, and also have one extra vacuum fitting for the fuel pressure regulator. Also on the 99-02s the vent hose from the passenger side valve cover went to the throttle body, on the DBW intake manifolds, it goes to the manifold itself right behind the throttle body (if you're using your DBC throttle body, there will be some clearance issues there). The '05 manifold also won't have all of the threaded brass things for the throttle cable bracket. At least those were the differences I found.

You can make it work pretty easily, but if your old manifold is good, it'd just be easier to use that.