If you haven't done the swap and don't therefore don't know the correct answer, don't give out wrong information
And yes, some people at work have p!ssed me off doing same today and I'm having to fix that too.
@remington115: There are 5 versions of the M5OD-R2 for 2WDs: 2 are Super coupe and I know limited about them, the 4.6 one only bolts to modular engines, so won't work behind Explorer engine. The pre '97 version of the R2 bolts to 5.0 (it was found behind 302s in F-150s); it is slightly less desirable as it puts the shifter right against the dash. But as it was bolted to 302, it has 1/2" holes on the bellhousing so bolts right up. The '97 and later version is slightly more desirable as it puts the shifter in exactly same location as the M5OD-R1. But it was bolted to the 4.2 V-6 using 12mm bolts - which are 0.7mm too small for 1/2" bolts needed by Explorer V-8. So you need to ream (drill) out the holes for 1/2" bolts. Note: The bell housing is integral to the transmission - one size fits all.
I went with '96 F-150 302 flywheel/clutch/starter as all the pieces fit OEM. Mine is custom balanced for 331, but make sure you get the right one (28 vs 50 oz imbalance).
When you get the transmission, remember to get the dust shield - they aren't sold by Ford anymore and PIA to get after the fact. You will also need a 31 spline yoke for the driveshaft - the 25 spline one you have isn't going to fit. But the R2 and R1 transmissions are same length so swapping yokes (tell yourself opportunity to replace u-joints) is all that is required.
The clutch hose connects to the R2 without issue.
There weren't any manual transmissions sold with V-8 Explorer, so you will need to adjust wiring to connect the transmission and you will need to have a tuner remove the automatic functions (and check engine light) from the computer.
If you have other questions, please ask.
p.s. If you want to got with T-5 out of Mustang. a. you will need to rig up a external slave cylinder to replace the cable solution. b. The shifter is right against seat - you will have to cut out floor to fit and maybe center seat if short legged/using 60/40 seat. The solution to that is to get the tail housing from an S-10 and swap it in. That puts shifter back in OEM location.
I like the 3.91 1st gear of M5OD-R2 as I use my truck as truck occasionally, while T-5s for V-8s are 2.95 and don't cut it for towing (but the T-5 shifts better for a "sports" truck).