You're going to want to read up on the DateTime class as Jason mentioned. It has a ToBinary method which you have used to convert the time to a long. Do the reverse of this when you want to convert your binary data back to a long. Which is 'FromBinary'.

C# has a nice class called "Convert", which has a few methods to convert one data type to another. In this case you want to convert the string from player prefs to a long (Int64). Now you can use the FromBinary to get the DateTime.

Once you have your old DateTime, you can use it's 'Subtract' method to subtract the new from the old. This gets stored as a TimeSpan variable. So check that out, and use it how you wish. See the below example.

Be careful though! As you can see, you're grabbing the old date from player prefs and then trying to calculate the difference. But what if this is the first playthrough? You need to take this factor into account. Perhaps set the old date to current date if there is none? Resulting in a difference of 00:00:00.

Enjoy!

using UnityEngine;
using System.Collections;
using System;

public class DataMaster : MonoBehaviour
{
    DateTime currentDate;
    DateTime oldDate;
    void Start()
    {
        //Store the current time when it starts
        currentDate = System.DateTime.Now;

        //Grab the old time from the player prefs as a long
        long temp = Convert.ToInt64(PlayerPrefs.GetString("sysString"));

        //Convert the old time from binary to a DataTime variable
        DateTime oldDate = DateTime.FromBinary(temp);
        print("oldDate: " + oldDate);

        //Use the Subtract method and store the result as a timespan variable
        TimeSpan difference = currentDate.Subtract(oldDate);
        print("Difference: " + difference);

    }

    void OnApplicationQuit()
    {
        //Savee the current system time as a string in the player prefs class
        PlayerPrefs.SetString("sysString", System.DateTime.Now.ToBinary().ToString());

        print("Saving this date to prefs: " + System.DateTime.Now);
    }

}

Add using System; to the top.

From there, you can start easily using DateTime objects to store, restore, and compare dates.

For instance:

DateTime currentDate;
currentDate = DateTime.now;

Would get today's date and store it in variable currentDate.

And these DateTime objects have all sorts of yummy things to play with, including a "DateTime.CompareTo" function. So you could do something like currentDate.CompareTo(lastDate); and get something useful out of that.

I'd recommend doing more reading about DateTime on other C#-related sites, but this is what I've been using and it works well.