I don't count the whole top-16, but for the current top-8 I have a few differences (the calculation is stopped after Roma, which is relevant for the RG seeds : Berdych can count his points from World Team cup for instance) :
Federer 6875 (15 points from DC play-off)
Del Potro 3010
Maybe I calculated wrong.
For Ferrer, for instance, I got:
3930 from GS, masters 1000, and World Tour finals
1430 from Valencia, s-Hertogenbosch, Bastad, Aukland, Kuala Lumpur, Doha
What did I miss out?