Seems simple enough to run the fan if you can get around the diagnostics tripping. Why not just have an ignition line drive a low side FET to ground the PWM signal to turn the fan on at key on.

For the diagnostic workaround and since the depth of my microprocessor knowledge stops at PIC16’s and I’ve avoided Arduinos just because I don’t feel like learning something new, I’m thinking a simple solution of either using a PWM to voltage conversion circuit and an Voltage/analog to Frequency converter might work well enough. Would have to do some digging on setting up ranges of Fan RPM diagnostics compared to PWM input.

Or it literally could be a simple as taking a 3” computer fan that has a PWM input and tach output and tuning it so the fan spins at the expected RPM then tucking that up in the battery space somewhere to trick the computer while the squirrel cage fan runs on its own.

NiMH DISCHARGE, 6.0A 6.00V Here is what the NiMH DISCHARGE page will look like before starting a discharge. You can set the discharge rate (6.0A) and the final voltage (6.00V) by pressing the right-most button and using the 2 middle buttons to increase/decrease the value. Then press the right-most button again to go to the next value adjustment. Once ready to start, hold down the right-most button.
NiMH CHARGE Aut, 2.0A CUR LIMIT Be sure to use the Auto charge mode and not the manual mode which is next in the menu. You can set the charge rate (2.0A) by pressing the right-most button and using the 2 middle buttons to increase/decrease the value. Once ready to start, hold down the right-most button.

NiMh Sensitivity, Delta V Default. I left the DeltaV sensitivity at 4mV which is the Default.
NiMH/NiCd Check Delay 0min I'm not too sure on what this setting does but I believe it is related to the DeltaV above. I left it at 0min.
Safety timer ON 230min Set the time limit to 230 minutes. At 6A discharge rate, it will only take a max of 1 hour to discharge a brand new module with 6Ah capacity. Obviously your old modules will take much less time to discharge. For charging at 2A, it will allow a module to charge up to 7,600 mAh which no module will ever reach unless you are doing some type of reconditioning, which i wont get into for this post.
Capacity Cut-Off ON 6000mAh I highly doubt any of your modules will ever reach this value while charging/discharging but this will be a safety cutoff.
Watt Limit (W) CHG:AUTO DCHG:80 You need to go into this menu page to verify the Discharge limit is set high enough to where it wont limit your max discharge current. I set it to the max of 80W.

Directions
Download the attached blank Excel spreadsheet. I changed the last column of the spreadsheet to add a third discharge column (second full discharge). Only 1 full discharge is necessary to know the capacity of the module, but if you have time and patience, a second full discharge will confirm the first full discharge results.
When you open your battery pack, take a permanent marker and number the modules 1 to 40 starting with the one closest to the fan.
I recommend gathering the measurements in the first two columns at the very beginning (internal resistance and initial voltage) for all the modules and then discharging/charging/discharging/charging/discharging one module at a time. If you can delay your initial measurements until 1 or 2 weeks after removing the battery from the car, that will give the worst self-discharging modules some time to discharge.
So once you have measured all the initial voltages and internal resistances, you'll begin performing the following steps for each of the 40 modules:

Initial 6A discharge to 6.0V. (Spreadsheet 1st Discharge) This will give you the capacity as removed from the car, not the FULL module capacity. The battery control module tends to keep the modules charged somewhere around 60-70% of their full capacity. Once this discharge is done, write down the mAh value given on the second line of the charger display. Wait 10 minutes before continuing to the charge step.
Auto Charge at 2A. (Spreadsheet 1st Charge) This will fully charge the module to prepare it for the next discharge. Write down the capacity (mAh value) given on the second line of the charger display in the appropriate column. This is how much power over time was input to the module. Wait 10 minutes before continuing to the next discharge step.
First Full Discharge (Spreadsheet 2nd Discharge). Same 6A to 6V as before, but you should expect to see a higher discharge capacity. This is the important measurement, so write down the capacity given on the second line of the charger display.

Now you have 2 options:
1) Repeat previous 2 steps on this same module to verify capacity and enter the charge/discharge capacities given by the charger into the spreadsheet in the 2nd Charge and 3rd Discharge column, or
2) Continue to the next module.

I did not select option #1, but did spend time trying to recondition some of the modules. If you do decide to verify the capacities, it will be beyond what I did and serve to provide better data.

To help you make a decision, calculate how long it took you to do the 2 previous steps and multiply that time by 40. Are you willing to spend that additional time overall for extra verification of capacity? if your modules are as bad as mine were, the discharge/charge process wont take very long (<1 hour). but if they take any considerable amount of charge, you will struggle to get through even the minimum first 2 steps for all the modules. Maybe you can decide on a threshold capacity that will trigger an additional verification. Like if you were to get any with over 3000mAh capacity, that might be worth verifying.
You can decrease the time required by using multiple chargers, but unless you have other uses for these chargers, you would need to buy and then sell them.