Shoggy, new EK D5 PWM ver2 work, EK changed the spec to meet the Intel standard (I run 2 with a splitty9) Not sure about the Alphacool D5's but maybe they have changed there's too? Maybe a sticky with which D5's work would be good? Bas66 you'll need an Aquaero 6XT, it has 4 PWM fan headers.
Can't seem to find out what spec the Alphacool D5's are, however there site does specify that VPP655PWM may not work with todays newer mobo's using adapter cable article number 52124 and connecting the pump to a fan control will work, again however I can't find this article 52124. If your pumps don't work you'll have to call them and ask or do as Shoggy suggests and mod the PWM cable on the D5.
Edit: Article 52124,
Pump connector