My son had an engine replaced in a '01 LS. Now the car wont pass emissions. on 2001 Lincoln LS

Engine came from a Jaguar(that's all we know) and it is giving random codes like different cylinder misfires and bad oxygen sensors although they were all replaced. Mechanic said there was a problem with the harness. Any of this makes any sense to anyone out there?

Asked by for the 2001 Lincoln LS
wow you need to have him double ck everything. on some imports the engine looks the same but the electronic are diff. good luck