Hi, I had some trouble with first myself:
You open a git shell and clone as in step 1, in step 2 you only need to run setup.bat, don’t compile the engine just yet. In step 3 you go back to your git shell and type the command to go to the flex branch. Then again in the git shell type the command from step 4. Then in step 5 you generate the projectfiles and compile the engine, NOT run setup.bat again since it will override some of the flex files.
If does not work, it might be because the branch on the gameworks github has been updated to 4.13.2 with hairworks??