Are you still running the turbo on the 240 motor? If so, dial back the boost a little (via the waste gate).
Did you swap over all of the sensors between engines? They should be identical, but you never know what someone did to an engine before you got it.
I'd put the car back to how it was electrically.... then troubleshoot from there. The turbo computers should run the NA engine. They should also give you a little insight via the OBD codes (check the 700/900 FAQ for how to get them - no tool needed).
What's the fuel pressure? Since you have fuel and spark, it's got to be a mixture thing. I think I'd suspect a coolant temp sensor or AMM. Is the turbo plumbing 100% good... without vacuum leaks?
-Ryan
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