As my factory is in high water use and low water risk, in this case, do I need to complete level 2 and 3 questions? (In FEM 4.0 guideline: Yes, but in self-assessment questionnaire: No.)

High Water Use and Low Water Risk, the facility needs to complete Levels 1,2 & 3, if they complete all Level 1 questions with positive answers.
(Yes or Partial Yes Answers), 

Based on the response to the applicability questions, facilities will be classified as a high or low water user, and a facility in an area of high or low water risk as follows:
Facilities with low water use (defined as using less than 35m3 per operating day) 
Facilities with high water use (defined as using equal to or greater than 35m3 per operating day) 
Facility located in an area of low water risk (as defined by the WRI Aqueduct Tool or the WWF Water Risk Filter).
Facility located in an area of high water risk (as defined by the WRI Aqueduct Tool or the WWF Water Risk Filter).

Facilities that are classified as either high water users or located in an area of high water risk (or both) will be asked to complete all FEM questions in the water section. Facilities classified as low water users that are located in areas of low water risk will only answer Level 1 questions.