[ganda1f]

Can you tell if the engine is getting flooded or starved for fuel?
Is your ignition timing set at 10 degrees BTDC with the engine warmed up and E1 and TE1 jumpered?
Some sensor being bad? Poor connection would normally trigger a CEL.
Coolant temp (not the one for the gauge sitting on the water-pump to head neck, but the one for the ECU), throttle position, MAP/MAF?
Perhaps try replacing them with the sensors from the old engine?