Yes it will fit, I have done two of these conversions, both with the Mustang EGR spacer.
You do have to buy a larger EGR spacer 70mm or expand the factory one.
I also use the mustang throttle cable on this set up.
The 4 studs needed for holding the TB/spacer to the upper plenum can be found at Summit and other Mustang vendors. They, old ones, usually are a little toasted. You usually have to do a little grinding on the upper plenum to insure the EGR spacer center hole lines up. And a little grinding on the small EGR port. I use the 96 Explorer gaskets for TB and EGR spacer.
Typically, I take the Explorer 65mm TB and change out the spring and shaft arm to one from a mustang 60mm TB. Occasionally, I will find them at the wrecking yard or I have friends who are happy to get rid of them, since they upgraded their rig to larger ones. Hard to find a Ford Racing 65mm one from back in the day when they were available...
On the first picture, I used a 98 MAF that has the ACT built into it, a little cleaner than drilling another hole in the intake pipe for the Explorer one. Minor change to the wiring to make it work. You do need the 6 pin plug from the 98 as well. If you don't go that route, I will need to dig up the part number of a grommet I used that is from the Dorman Help line.
The 96 heater cooling tubes work the best to retain the Mustang EGR coolant cooling hoses. A little more creative routing with the hoses, and I typically use 1/4" silicon hoses with EFI hose clamps with the hope I don't ever have to replace them.
There is other little fine tuning items like making a bracket for the EGR vacuum controller, I can't recall if I used the mustang EGR valve with the Explorer EGR sensor (Interchangeable) or the other way around. It is all about what fits and how long the pigtail on the harness is.