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Yeah, the 5E is a DOHC, but both cams are turned by the same gear. So it works in a similar way to a SOHC but has the better flow of a DOHC.
In any case, whether a 5E ecu will work on a 3E or not (I don't have that answer btw), it won't give you much, if any, performance increase at all. All E series motors are tuned for fuel economy and reliability. The only way to get a good increase from an ecu upgrade is to get it reprogrammed, or use a stand-alone ecu. But those should be considered last resorts. There are many other upgrades that can be done, for significantly lower cost.
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