The second O2 sensor is putting the EML on as it is not seeing the correct range of figures from the cat. This is happening because the cat is not there.

To fix this, you need to either put the cat back or get the O2 sensor coded out of the ECU. Bear in mind though, that come MOT, you need to put the decat back on as it WILL be tested for it now, i.e. if fitted from new, it MUST be there now.