I prefer matching barrels, but at a pinch, I'd put the '16 barrel (with its '16 RC valves) on, with the '18 head (If its not damaged) and just run it at that.
Scary news: My MC18, when I had the '16 barrels on it (MC18 heads, carbs and electrics), wasn't much slower than another NSR MC18 that was poking around . And I made up the ground under brakes
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The Chopster