Here it's good to note that Kirk in two universes is called Cadet and carries no signs of commissioned rank when trying to complete his supposed Command studies by tackling the no-win scenario
Yes, McCoy's line about about Kirk being a cadet when he took he the KM is the one thing I have to disregard. But since Kirk taking the test in Command School in 2258 fits so well in every other respect, I'm fine with that.
Instead, study packages ranging from three to five years have been seen, without much comment (beyond "You could be an officer in four years" / "I'll do it in three"
If Starfleet Academy is a four year institution and you graduate with the rank of Ensign, you're an officer after four years.
...Why make "WNMHGB" part of the 5YM at all, though?
As I said above, backdating WNM to before the 5YM creates more problems than it solves. You have to have the 31-year-old Kirk make Captain even
sooner than he already has, which begins to stretch credibility to the breaking point.
And then you have to shift Kirk's first meeting with Gary Mitchell ("a man I've known for 15 years") back as well to preserve
that time reference. If Kirk assumes command in 2265, he met Mitchell in 2250, the same year that they both entered the Academy ("Gary told me you've been friends since he joined the service"). If Kirk assumes command in 2264 or even earlier, you either have to invent an entirely
new time, place and reason for Kirk and Mitchell to meet, or have Kirk entering the Academy at 14 or 15.
WNM is important, sure, but not so important that I'm going to tear apart half of my timeline just to place it before the 5YM. It fits into the 5YM just fine, so into the 5YM it goes.
I put this right before Kirk's 32 birthday making him 31, the youngest Starship Captain in Starfleet.
I also have Kirk taking command at 31 in my timeline. Born in 2234, takes command of the E in April 2265, right after he turns 31, breaking the previous record of making Captain at 32 set by Christopher Pike.
I go with the idea that the crew in "Where No Man Has Gone Before" is the one Kirk inherited from the end of Pike's time. Anyone who was in the rest of TOS but not WNMHGB is one of Kirk's people.
I certainly think that Kirk's initial crew had some carryovers from Pike's crew. Spock of course, and Scotty and Piper seem likely to be Pike people as well.
BTW, I currently have Mitchell coming on board Pike's
Enterprise in 2263. That way he can serve next to Mr. Spock "for years," as per WNM. Dehner says that Kirk
requested Mitchell for his first command.* She didn't say that Kirk got him.
(*The USS
Saladin, which Kirk got as a Commander.)
As for the refit question, nowhere is it written that a ship
automatically gets a refit whenever it switches Captains. "The Cage" takes place in 2254 and WMN takes place in 2265. Plenty of time in those 11 years for the
Enterprise to get a refit under Pike's command to explain any set differences between the two episodes. And since there are even
more set differences between WNM and "The Corbomite Maneuver," I think it makes a lot more sense to put any refit under Kirk's command
after WNM than before it. (And it doesn't have to take up a year or more, either.)