Couple of things to check -
Are you getting voltage to both fans when they should be on (as per the linked discussion on the P0480 code)? You can check the volttages at the fan power connectors with them removed from the fan.
You also can see if the fans will run by unplugging their power connectors and feeding in 12 volts directly to the fan with clip leads from the battery positive terminal, and another clip lead to the engine block. Make the connection to the block last, you might get a good sized spark as the contact makes, you don't want to make the last connection at the battery (just like when you jump start a car) or you might get an explosion from any hydrogen venting from the battery..
If you have voltage going to the fans at their connectors, they should run, unless you have a high resistance in the wiring somewhere, most likely on the negative (ground) side of the circuit, OR the fan that doesn't run has worn commutator brushes which is preventing it from running. That should show up when you try to run it right off the battery.
If you are not getting voltage at the fan power connectors when you should have the fans on, I would check the fan relay. The fan circuit fuse is probably OK because you said at least one fan comes on, they are both fed through the same fuse.
Before you go out and buy a new relay, try taking out the original one, spray some contact cleanr in the fuse panel connector side, and on the relay pins. Cycle the relay in and out a few times to wipe the contacts.
You can check to see if the relay is picking up to turn on the fans by putting a mechanics stethoscope on it to listen for it clicking. If you don't have a stethoscope, use a long shafted screwdriver as a listening rod, with the tip on the relay, and the handle mashed into your ear.
On my 2001 SE 3.1, both fans always come and go together, I usually keep the AC mode on so they will cycle more often to keep the temp excursions down in traffic and when doing extended idling.
Have you checked the actual coolant temps with an IR laser scanner on the thermostat housing, or with a diagnostic scan tool that reads live data? What is your dash temp gauge reading? It should be stable around 195 degrees, and at idle on a warm day, should slowly creep up until the fans kick on to pull it back down.
