93 Cobra lower intake and 98 explorer upper?

They should match. The lower for the Explorer looks to be the same casting minus a couple of machining operations. There is no water connection at the rear passenger side for the EGR lines; there is no tapped hole in the number 5 (I think -- front driver side) runner for the (I think again) air temperature sensor. And I'd have to go look for an EGR passage, since the explorer did not have the EGR valve in the same place. My buddy and I successfully tapped the correct holes in the Explorer lower for use in his Mustang-based Factpry Five Cobra.
 
I did essentially that on my 351 w/Ebrock Perf 1.9 heads. The lower was a GT40-351.
The Explorer upper was just a tad smaller diameter than the bottom, but less than 1/2 hour work with a sanding roll opened it up and blended into the ports for an inch or so to perfectly match.

Even with a mild motor (see sig) I'm very happy with the performance and the torque curve.