Can you teach a still developing clone science and every other bit of education they need in 5 years?
Yes.
... I mean, so far all of the other excuses are made-out-of-whole-cloth-pulled-out-of-hammerspace fiction. There's nothing that says "the fiction works this way, not that way". The fiction works, however the writer says it works.
So if they're cloning the Colonel, the narrative says cloning is possible. Without that added bit of info someone who said "Why didn't they just clone his brother" could have been met with scorn and dismissal: You can't just clone someone!!
But, turns out you can. Now "why didn't they just clone the brother" is a logical question within the narrative. If they introduce time travel, "why didn't they just go back in time to stop the mugger" becomes a logical question.
I'm sure the Col. won't be a completely different person just with the exact same body. Now he's a pediatrician who collects butterflies. He'll somehow know or remember, he'll be reprogramed. Then we go by the narrative. Reprogramming takes 10 years, 3 weeks, 2 days and 4 hours. Reprogramming is automatic, like putting in a DVD. It's whatever they say it is.
Jake is chosen for the job based only on his genetic make-up. I submit to you he's no better suited for the task than a xerox of his brother who lacks higher science education. Until the narrative says otherwise... It takes $5 billion and 1 dollars to make a clone and it's just cheaper to have his idiot brother pilot the $5 billion dollar Avatar. Someone spilled a Red Bull on the flash drive that had his brothers genome sequenced. Whatever the excuse will be.
Again, I harp on "reason" vs. "excuse". There are an infinite supply of excuses.