Yes it will...with a few caveats. The problem is, Ford never put a manual trans behind a 5.0 in an Explorer. that means you could have ECM problems where it's all integrated with the automatic trans. Will that cause an issue? Not sure. Can it be tuned out? Call James at Henson Performance. Another option would be to look for a 1996 Bronco or F150 that had a manual trans behind a 5.0 and see if you can get an ECM for that. The secret here is you have OBDII in the 98, so that limits you from going to something like a Mustang ECM which is OBDI (EEC-IV) Keep in mind using any processor that is earlier than the year vehicle you have is technically illegal. Whether that would show on an emissions check or not I don't know. Can they see the year and calibration of the processor? Possibly.
Next thing to worry about is whether or not the crankshaft is drilled for the pilot bearing. Believe it or not, manufacturers get cheap and if they know an engine will never receive a standard trans, they won't drill or finish machine the crank for a pilot bearing. I just had the crank out of a 99 and didn't look either damn it.
Then you have the problem of locating the shifter through the floor board. You will have to go probably get your hands on a standard trans Explorer and rob the tunnel cover, boot, etc. That part should be easy. You will also need a clutch activation set up. Rob from the same Explorer as the tunnel parts...or just hang a clutch master cylinder and pedals and use a McLeod bearing.
Finally, if this is a 4WD, you need to come up with the adapter for the transfer case, and you will have to swap out the transfer case for a different one...4406 would be my first thought. Drivelines, shifter, etc would be needed. This really should be a great swap. I want to see someone put a T56 in one.