Poor HVAC Controls
 

So the blower fan stopped working on all positions except for #4 (high) on my daughter's 2000 Protege. I replaced the resistor card that connects to a harness and is fastened into the large plenum behind the dash. The system worked fine for only a few hours then the fan stopped working again on positions 1-2-3. Also, the heater doesn't appear to produce full hot air and the green AC light has gone intermittent. Rather than put another resistor card in (and waste another $50), is the HVAC control module most likely the problem? How can I verify that before chasing down a unit at the auto wreckers?

Yes. The blower switch is the most likely cause of the trouble. I referred to that in the "Unofficial User's Guide to the '95-'98 Protege". I suppose Mazda did not fix the issue in the later model years.
In most cases the switch does not move smoothy because a single internal spring is causing uneven pressure between moving parts. Someone reported he opened the switch and put a second spring and ball in there to fix it for good.

If it consoles you: I have wasted money on a resistor as well.

check the fan switch

Pulled the car back out of storage earlier this summer (my daughter returned from university) and ended up buying a used HVAC head unit from the wreckers for $75. Figured out how to remove the front dash trim bezel and removed the old head unit by disconnecting the 3 cables from their respective control units. Once reassembled, I noticed that the "AC on" button now lit up in all 4 fan speed positions (old one would not do that) and the compressor was definitely working but the fan still only worked on high. As I had already put a new resistor card in last summer (only to have it burn out in a few hours), I removed it and put another new one in ($55 later!). Voila; everything now worked perfectly fine. Added a small can of coolant into the system for good measure.

Next day my daughter texted me saying "she got a brain freeze coming home from work"! That made it all worthwhile! Kept the old HVAC unit so as to dismantle it and learn how it failed.