Have you determined if the transformer has failed again? If so, list the screw terminals on the circuit board with thermostat wires connected - is "C" used? Does the system have a humidifier? We can probably ignore any possibility of any shorted line-voltage wires since the blower does run. Also, check the mounting of the circuit board. Dismount it and look for evidence of arcing against the enclosure. Assure that top edge of board is properly engaged in tabs on enclosure - they should alternate/stagger.