how can i number each user input? C#

There are a lot of data structures that will allow you to store data in order. I'd personally recommend a List<int> for this.

You can add things to it as simply as:

var list = new List<int>();
list.Add(37);
list.Add(95);

And you can either read it with an iterator (foreach(var score in list){...}) or get individual numbers out (var firstScore = list[0]). The documentation will tell you more about what you can do with a List<T>.

declare one variable to count inputs like private static int counter = 0;
in InputGrade method, put like below

Console.WriteLine("{0}\n{1}",
                "Enter the integer grades in the range 0-100",
                "Type <Ctrl> z and press Enter to terminate input:");
counter++;
System.Console.Write("score " + counter + ":");
input =  Console.ReadLine(); //read user input

and inside while (input != null) put like below

IncrementLetterGradeCounter(grade);
counter++;
System.Console.Write("score " + counter + ":");
input = Console.ReadLine();

so, output will be like

Here is the full code

    public class Program
    {
        private int total;  // sum of grades
        private int gradeCounter; //number of grades entered
        private int aCount; // Count of A grades
        private int bCount; // Count of B grades
        private int cCount; // Count of C grades
        private int dCount; // Count of D grades
        private int fCount; // Count of F grades
        private string v;
        private static int counter = 0;


        public string CourseName { get; set; }

        public Program(string name)
        {
            CourseName = name;
        }

        public void DisplayMessage()
        {
            Console.WriteLine("Welcome to the grade book for \n{0}!\n",
                CourseName);
        }

        public void InputGrade()
        {
            int grade;
            string input;

            Console.WriteLine("{0}\n{1}",
                "Enter the integer grades in the range 0-100",
                "Type <Ctrl> z and press Enter to terminate input:");
            counter++;
            System.Console.Write("score " + counter + ":");
            input =  Console.ReadLine(); //read user input

            while (input != null)
            {
                grade = Convert.ToInt32(input); //read grade off user input
                total += grade;// add grade to total
                gradeCounter++; //  increment number of grades

                IncrementLetterGradeCounter(grade);
                counter++;
                System.Console.Write("score " + counter + ":");
                input = Console.ReadLine();
            }
        }
        private void IncrementLetterGradeCounter(int grade)
        {
            switch (grade / 10)
            {
                case 9: //grade was in the 90s
                case 10:
                    ++aCount;
                    break;
                case 8:
                    ++bCount;
                    break;
                case7:
                    ++cCount;
                case6:
                    ++dCount;
                    break;
                default:
                    ++fCount;
                    break;

            }
        }
        public void DisplayGradeReport()
        {
            Console.WriteLine("\nGrade Report");

            if (gradeCounter != 0)
            {
                double average = (double)total / gradeCounter;

                Console.WriteLine("Total of the {0} grades entered is {1}",
                    gradeCounter, total);
                Console.WriteLine("class average is {0:F}", average);
                Console.WriteLine("{0}A: {1}\nB: {2}\nC: {3}\nD: {4}\nF: {5} ",
                    "Number of students who received each grade: \n",
                   aCount,
                   bCount,
                   cCount,
                   dCount,
                   fCount);
            }
            else
                Console.WriteLine("No grades were entered");
        }
        static void Main(string[] args)
        {
            Program mygradebook = new Program(
                "CS101 introduction to C3 programming");
            mygradebook.DisplayMessage();
            mygradebook.InputGrade();
            mygradebook.DisplayGradeReport();
            Console.ReadKey();
        }
    }

You can look for Collections available in C# (MSDN Collections).

In your case, you don't really care about order, you can use List<int>. Otherwise if you want to keep an order you can use Stack<int> or Queue<int>. And if you want to keep a collection of Student Name + Score you can use a Dictionary<string,int>