I've done the same, MC18 top end on a 16, except it was in an MC18 chassis.
You'll know if it is an MC16 engine in the '18 chassis, because you have to take 8mm off the sprocket side of the rear upper engine mount for it to fit and the chain to line up.

But I had the 18 top end and pipes on it.
Come to think of it, I just had the MC16 engine in it for a while, with the '18 electrics (PGMII) and the MC18 pipes and heads, before I got the MC18 cylinders.
Note: The MC16 RC valve servo (needed for the MC16 cylinders) runs BACKWARDS with the MC18 electrics!
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The Chopster