If my understanding of the way the circuit works is correct, even with main fan relay 2 removed, when the engine temp is above normal, main fan relay 1 should have activated (i.e. the ECM is setting the fans on high speed), turning the main fan on, while the sub-fan would remain off due to the absent main fan relay 2. (A bad main fan 2 relay would affect the slow speed of both fans due to its role in the series connection, and the high speed of the sub-fan due to its routing the ground for the sub-fan, but not the high speed of the main fan.)
Looking at the main fan relay1, if it is bad (or, for that matter, removed), it wouldn't affect the slow speed operation, nor the high speed function of the sub-fan.
Similarly, if one fuse is out, it might affect one aspect of the fan operations, but not both. It would require at least two fuses, one in each high speed circuit, to be open for there to be no fan operation at all.
So while the wiring circuit for the fans appears overly complex, in some ways it has built in failsafes and possible diagnostic indicators.
Because neither fan comes on even when the engine temp is above normal, it has to be something common to both the slow and high speed arrangements. In this regard, there's still the common ground that should to be verified, along with the connections to the motors (connect and disconnect a few times and see if that changes anything), and the motors themselves.
In regard to the motors, have you tried manually spinning the fans (ignition OFF) just to get the motor rotors into a different position? Also, it should be possible to measure the resistance across the motors at their two-pin connectors. The resistance should be low (if the motors are open circuit, the resistance reading will be high) and when the fan is manually turned, the Ohmmeter reading should jump around (due to magnetically induced voltages).
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