My 1st thought after reading your messages is that you should just go out and buy a CS... Seriously, if you want an F1 car and you don't want to butcher your mint low mileage 360 its a serious question you need to ask.
My rationale comes from that you seem to be fixating about little details like if the engine pistons are exactly the same yet the bigger picture is you'll get much better (noticeable) gains from say Sports cats across the entire rev range too.
The truth being it will never have a CS chassis number so you'll never get it 'exactly' the same and it seems like your trying to get it exactly the same no matter what the cost. Purists will always look down their noses at your 'replica' - even if its cost hundreds of thousands to get 'exactly' right.
If however your had the clear goals to improve on it, and lets be honest there are many areas which this is possible, especially today, then you can get a car that not only handles better but is more powerful, have lower weight and will be a joy to own.
I actually have the Ferrari factory Challenge Stradale Technical lead as one of my LinkedIn friends so if you would like to know what Ferrari would have done with unlimited budget I have the means to ask questions directly....
Also lets be clear here there are little changes which make a big difference, e.g. the modification which comes from the 430 Scuderia which adds soft/hard mode damper switch independent of the race mode for engine maps/throttle response and f1 shift is also high up there in the real world as 'what it should have always had' and the list goes on... Back to the pistons thing, I actually said its simply not worth chasing the extra few hp's that the slightly higher CR yields (its less than 5hp) and most of that actually comes from the fact that they are properly balanced to 0.5% tolerances of the challenge program. By the time you've opened up the engine and done this its into big money for minuscule gains, you'd be better off spending the cash elsewhere as you can gain from other area's better bang for buck. If you wanted serious increases you'd be better looking at engine transplants rather than opening up the 3.6 which was already pretty efficient anyway.
The big money ticket is weight (or lack of it). You can junk as much as 250-300kg's out of the car if you are serious about it. That's huge and the difference in performance is just jaw dropping.
Strive for perfection in everything we do. Take the best that exists and make it better.
When it does not exist, design it. Accept nothing nearly right or good enough.