different thoughts, or different memories?
both are similar but on a whole different scale.
let's take three subjects.
A, B, and C.
A white caucasian, a black african and a yellow chinese.
The white is a fanatical catholical-nazi, the chinese an overzealous nationalist and destroyer of all religions, and the african is a fervent muslim of the heavy side of the religion.
(so, to say it bluntly, take three completely different people of three different ideals and faiths and the like)
now they all become A1, A2, A3.
they are all physically the same.
but their minds are different. their faith, and all that is not physical is kept.
While the "white caucasian nazi-catholic" might be fine, (nazism WAS the purity of race, if all the race are the same=only pure race remains).
but catholicisim might clash against a muslim, on female rights/wrongs (this is taking the WORSE possible of ALL the religions, mind you, so i'm only speaking in extremisms)
and the "nationalist" might clash against not only their ideas but the place they were born into, "i was born in greath mother china, i am better!".
So physical is one thing, but is not the complete answer.
Now you transform them again.
A, B, C
but you copy paste A, or B, or C mindpattern in the others.
what you obtain is best known as a multiple personality disorders, a Black african catholic nazist? (stressing the nazi, not the catholic part)
then they would start to purge each others, because they'd be an affront to themselves, maybe some might try and change their ways of thinking...
(disney reference anyone? you hate pandas, you become a panda, you start loving pandas otherwise you might end up stuffed on a wall?)
but in the end, it wouldn't change much.
Now you physically and mentally transform them all.
A, A and A.
while it might be bothersome not to recognise the original A in the middle, it's not like anyone is going to suffer from it.
being there "no sexuality" (we shall consider all three A's to be asexual, and reproduce through strict cloning system). the problem of "fighting" for procreation comes lest.
Now, the geograpichal collocation of said individuals might be a problem.
(let's say you're an A in europe, it's different from being an A in the saharian desert) but you adapt, we are all different as races/thoughts because of our adaptation to the live around us.
adapting makes you different, at first, but you just repeat the process through cloning. and not in the "superhuman" nieztche way of the term, were the rest should die.
You just start cloning the different with the genes of the adapted, all of them, and you create a new "batch" of clones all identical, all superior to the precedent generation, and you let the old one die in peace.
you repeat the process until you obtain precisely what is asked: a generation of all identical beings, of same skin.
For their intellectual part it's even easier. Starting from generation One you teach them all except religions, of any kind.
So only science and the like. Might be unfair for the faithful or the like, but hey, if a god truly exists he'll show his face again to this new guys who have no idea what a god is.
So generation one grows without knowing religion.
generation 2 even.
and you procede like that.
Then you simply place in front of them a plan a grand plan, not a tiny little one, one that can concentrate their resources to the limit, like:
"Conquer the ENTIRE galaxy". (longer and harder plan? better!)
in this way, providing you give each of them the same exact things, (like one spoon to each, one bed to each, one teddy bear to each) they will grow identical in some but not all experiences...
(the possibilities of having a tooth ache or a stomach ache cannot be discerned, obviously).
but you do not need to synchronize their thoughts.
You could create such a feat and use it as a sort of "corrective" measurement, if ever need their be in a society which should be "perfect" as the question asks.
in that way a criminal (of what? self murder? you just clone it again and his fine alive) get resynched with the thoughts of the best worker/soldier/control unit, and is back to work.
Obviously his mind is searched to understand what made him stray, and things get corrected.
in this way you achieve peace, tollerance and everything nice:
Complete annihilation of everything wrong, where wrong is marked as anything different from the "best possible outcome, in the best possible world" like in Voltaires candide.