The bottom end is for all intents and purposes the same, the one thing that you will have to check is the presence/absence of a bung for the knock sensor in the 99 block. I am not sure when the casting was changed, but i do know what the bung remained in blocks long after the demise of the renix injection.
As for the top end, the port design changed from renix to H.O. years (the ports became taller) so the older intake wont line up *correctly* with the newer head ports. If you use the newer intake manifold, then there will be no port for an EGR valve (which is useless garbage anyway) but if your shop is going to check for smog equipment...
Also the older TB won't bolt up to the new intake and sensor swapping between them is a bit tricky. You could machine a spacer plate if you went this route.