D1 and D2 set up a reference of about 1.4 volts on the "-" op amp input.
The two diode reference voltage will vary a bit depending on the diode current and temperature.
The value of R3 is not very critical but it should be low enough to pass a current that keeps the diode's forward voltage above the knee of the VI curve, the diode's forward voltage is more linear above that point up to a certain level. However R3 should not be so low a value that it wastes excess power, puts the diode into the non-linear part of the curve, or brings the current any where near the diode's max forward continuous current spec (Ifm). Using a chart of the diodes forward characteristics, (see datasheet for a 1N4148 ), determine a diode current Id near the assumed 0.7 Vf point then calculate an appropriate R3 value to achieve that.
The general equation for R3 will be:
R3 = (Vcc - Vf(d1) - Vf(d2) ) / Id
R9 will determine the current through LED D4. But you should also know Vf of the LED, the desired current level for the LED, and what the minimum level is for Vcc.
The general equation to find R9 will be:
R9 = (Vcc(min) - Vf(d4)) / I(d4)