Not to rain on anyones parade, but it has been said repeatedly in these forums that any 'Pima less than 8 inches is going to be hard to raise.
Have a look in any of the big Arapaima threads and you'll find reference to this.
There method of reproduction involves a certain period of time where the fingerlings feed from their father - much like discus fry - and to pull them too soon can leave them with weakened immune systems etc.
I read this whole thread and while I can agree to some extent on the tank size issue, in my opinion (and remember, I've never owned a 'Pima) it sounds like a combination of factors.
Tank size is one, but I think if the 'Pima had been on it's own in there with good water parameters, it would have been fine for a couple of months.
It's likely that while appearing healthy, it was just too young to be put in with other fish in a tank that size. a little bit bigger and it may have been able to handle itself.
I think the poor thing just got stressed out at such a young age and that's why it died.
Comments on my humble opinion are most welcome.....