There are guys that have made the SOHC engine work with a DOHC ECU, but it's not easy, and I've never found any definitive "how to" discussion. It seems the sticking point is some of the sensors - specifically the IAC, which is a completely different type on the two different engines.
One option you could look into is using the SOHC shortblock with the DOHC heads, intake manifold, and associated sensors. It'll bolt right up, and you'll get a slight bump in compression ratio as an added benefit. Obviously that's going to take more work on the mechanical side, but it will save you from doing any work on the electrical side.