My 2000 has never had any problems with the heater / evaporator unit other than the common stink that can form in warm high humidity conditions.
When you installed your new mode control motor, did you check the position switch contact operation as described on 22-91 of the 1991 service manual as you run through the control motor operation? If something is preventing the doors from moving correctly the switches may not be sending indication back to the CCU and it may be keeping the motor powered up leading to a short life.
The instructions for replacement of the mode motor are minimalist. There does not appear to be any provision for adjustment like on some of the other motors. The only thing it says to do is confirm that the heat and def doors move smoothly and that the motor does not pull the door too far; but, it doesn't say what 'too far' is. Before installing the new motor I would confirm that the heat and def doors move smoothly and after installation that the position switch is working correctly.