I've had two Explorers with manual transmissions, and both of them did not like Mercon V fluid before or after rebuilds. Ford says they are interchangeable and maybe in most applications they are, but it appears to be the wrong viscosity or has the wrong friction properties for smooth shifting in a manual transmission.
I would highly recommend multipurpose Dex/Merc fluid instead. GM has rebranded Dex III as "Manual Transmission and transfer case fluid" which the dealer (or Amazon) carries, but it's almost certainly just cheap Dex III fluid that you can get at Walmart. I just filled my rebuilt manual transmission with this and the difference between it and Mercon V is very noticeable. Mercon V was super notchy and with inconsistent engagement.
I've tried the fancy synthetic ATFs and oils (5w-20, 5w-30, synchromesh, etc) and none of them were as good as regular cheap Dex/Merc fluid or GM's manual transmission fluid.