IF and I qualify this statement "IF" there are any small changes to the fuel injection/electrical system, I would think the sensors should be swapped - meaning the sensors should match the ECU and not the engine. The basic engine is mechanically the same but if any changes to the ECU were made on the new model year, you want the correct sensors to work with the ECU. In your case, the 2001 engine is going into a 1999 frame. I would think you are using the 1999 ECU and harness already in the frame. So you use the 1999 sensors and swap them on to the 2001 engine before you install it.
The sensors might be identicle from year to year 1999-2001, but the FI system is different starting 2002 without a doubt. Check the part numbers on the sensors to ensure they are the same.