When replacing the head, there would have been no need to replace the manifolds, the originals will work (and would have worked) fine with a replacement head. In fact, I'd venture to say that it is rather unlikely that the manifolds were replaced.
I don't know from personal knowledge that the E48 manifold casting is correct for the very early cars, but I think it is.
Benefits to having an E31 instead? Performance and mileage will be very little different for a stock 240Z. I doubt it's worth it for these reasons.
But for value - on a fairly low VIN (early production) car such as yours, there would be some additional value to having the "correct" head on it, but only if the rest of the car is also "correct" and original. If it is modified now, and you have no intentions to restore it to original, the added value would be small.
If it were me, I think I'd keep my eyes open for a good E31 head just to have, I wouldn't worry about putting it on the car unless I were doing the restore-to-original thing. But at least that way you'd have one, whether for your own use in the future, or as a selling feature for the next buyer should you decide to sell.
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