Quite a few 'rasboras' or 'boraras' species would be suitable, even in water as low as 4.0 pH.
I don't think we want to stock with fish that can withstand low PH number. The reason behind my thinking is that your well water quickly outgases and the PH quickly climbs up to about 7.5. So If we have a fish that do best in acidic water the tank water prior to a water change would about 7.5. After the water change it would would be acidic, and then within 24 to 48 hours it would be 7.5 again. In my mind the would give the fish of a PH shock.
The best abroad in my mind is is to put the well water in a bucket and let it outgas until the PH stabilizes to about 7.5. Do the water change. And immediately after the water change the PH would still be 7.5. No PH shock. So if we do this most soft water fish would be suitable for your tank as long as they are small due to your tanks 6 gallon capacity. One fish you might be interested in is:
http://www.seriouslyfish.com/species/celestichthys-margaritatus/
GH: 75-150Well, that's the question... If the 40 you mention is 40 ppm, then its too soft... WAY too soft..
It should be noted that while the water is soft the tank water in this case is at a GH of 75 to 150ppm. So while going to direct well water getting soft water fish is one solution. The other solution is to reduce the amount of RO or distilled water you use and increasing the hard tap water you have. Boosting the water hardness this way would help the endless. However we also have the complication with your Oto and shrimp. We don't want to get the GH too high for them. Then the only other issue we have is why are your plants not growing well. Do the leaves of your plants look healthy or are you seeing holes or yellow leaves?