Something is obviously different now to when it was OK - has anything changed?

The Cossie ECU will only know there's a problem with most sensors if they're disconnected, otherwise it'll just do as it's 'told'. Check they're all connected (and connected the right way up! )

Is the fuel return actually blocked? Is the CO pot on the ECU in the same place it was before you took the engine out? Has the fuel pressure regulator been fiddled with?