If I remember correctly 'CHOICE' only works on 9x so try using this:
set /p user=Enter Y/N
IF %user% EQU N GOTO NO
IF %user% EQU Y GOTO YES
Instead of this:
echo Y Yes
echo N No
CHOICE /C:yn Choose an option.
IF errorlevel 2 GOTO No
IF errorlevel 1 GOTO Yes