You can either replace the tube with one having a longer Presta valve, or buy a valve extender from any LBS. They are dirt cheap and will do the job nicely. I have Spinergy xaero-X wheels, and have the same problem. The rim is made by FIR, and is a semi-aero 24mm deep section. I can get a pump on some standard tubes, but its an iffy proposition. The 60mm valve stems seem like overkill, so the extender (which does not stay on the valve, you install it to inflate, then remove it to re-secure the valve) works nicely. I keep one in every patch kit I own, along with a presta to schraeder adapter, so I can help out anyone, or get help from anyone.
DEMON