So your setup is going to have regenerative braking? Many DIY conversions don't due to the added cost of going with an AC system. Still, I think a 16kWh pack is prudent for 40 mile range. 6kWh is definitely not enough. Even with the streamlined CRX you will still use at the very least 200Wh/mile. This is perfectly flat ground, ideal road conditions, etc. Take a look at evalbum.com and see if anyone has posted Wh/mile ratings for their CRX, I found 240 Wh/mlie. That will give you an idea of how much power it will take you to get your 40 mile range. Keep in mind that you also do not want to cycle your batteries to fully discharged. For lithium you should definitely not take them lower than 80% depth of discharge (DOD), and 70% will give you much better life out of the batteries. So, you need to add an additional buffer there. Now, as the batteries age they will also loose capacity, so you need to account for that as well. All these things add up and in the end a larger battery pack is what is needed.
For the EV I'm planning (if I ever get around to it), I am using 500Wh/mile as a worst case scenario for winter driving (cold bearings/trans oil/heater/etc). This is with a Toyota Paseo which isn't a whole lot bigger or less aerodynamic than a CRX. With these conservative numbers I know I'll be ok after a few years and still be able to make my commute. Don't skimp on the battery pack.
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