As stated, look at the part # and if the upper has the EGR hole in the middle you are good. Mike posted this pic a few years back.
later model on the left early model on the right with EGR port
You have this lower? Does not have hole in the center of it for the EGR or the IAT boss on the #5 runner?
Your uppper looks like this, correct?
Sorry, you have the wrong lower if you want to maintain your factory EGR. You need to get the one that has the EGR provision and as stated is RF-F87E-9K461-BA, from a 93-97.
Are you asking will it fit? Yes. However, you will trip the CEL, have codes. To do it right, remove the EGR and get a blockoff or bypass plate, cap off the vacuum lines, plug the holes in the back of the heads, and get a tune for the CEL. IT will cost you a lot more to properly delete the EGR than to just buy the proper lower intake and sell the one you have. There is no performance benefit IMO in removing the EGR.
You'll either never notice a thing, or join the ranks of those wondering why the car idles poorly, has poor gas mileage and overall doesn't run right after disabling smog and emission equipment. I've seen plenty of each.
Can you possibly search out the correct lower intake and then sell the one you have? -BA lower would have the hole for the EGR and it would be a factory install.
FYI the explorer uses an external EGR, so the internal EGR was never used on the explorer. They are simply holdovers from its Mustang roots, so it's entirely possibly to get mismatched set ups from a transition year explorer (I believe 1997 was the year)