bz,
I'll be interested in what you come up with....my configuration is the same as you described, i.e one pressure gauge at the pump only. The diffussers are at different depths, also.
In dealing with compressible gas, the mass flow rate varies directly with pressure....but I haven't looked at those equations in years and I think my doctor told me I couldn't do that anymore.
http://exploration.grc.nasa.gov/education/rocket/mflchk.html