I don't think you can do that type of analysis here. For instance, in your calculation, Philippoussis's two Major finals garner him 2,400 points vs. 2,000 for del Potro, who won the U.S. Open.
Similarly, your calculation gives Rios 5,000 points for his five Masters Series shields, which makes those five shields better than the two Majors won by players like Rafter, Wawrinka, and Kafelnikov (4,800 points).
It seems much simpler to say that the three key criteria should be (1) performance at Majors; (2) weeks/years at #1; and (3) performance at WTF. If Player 1 has more Majors than player 2, they win under criterion #1. If they have the same number of Majors, we look to other finals, semifinals and quarterfinals. If Player 1 has more weeks/years at #1, they win under criterion #2. If Player 1 has better results at WTF, they win under criterion #3.
If one player in better under all three criteria, they're the better player. If there's no clear winner under these 3 criteria, we can look at other factors.