welcome!
a few things: 1st, you mention running the 12v water pump not through the inverter on a 48v bank... this assumes a center taping scenario?? IE: just chucking the water pump to two of the eight batteries??
if this is the case, it's a really bad idea. sure, it's a small power draw, but over long term, it is going to throw the whole bank off balance. equalizing the bank can help this, as well as switching what two batts you connect the water pump to, but all in all, it's a practice that isn't really worth doing. if you insist on using the water pump without the inverter on, get a dc to dc converter. it can take 48v to 12v and they can be found on the super cheap from ebay (china).
also, is there any solar? can you spend a few hundred bucks on some? the reason i ask, is the generator charging scenario. sure, the genset is great for pushing big amps in the "bulk" portion of the charge, but it still has to run for long durations when very little amps are needed for the absorb, and float portions of the charge. even a few small solar panels could eliminate this time/fuel consuming portion of the charge. i'll bet even a $1000 investment of solar panels and charge controller would pay off in a year or two, plus it would give you the added benefit of making the bank last longer due to more fully finished float charges per year.
have you checked the water level in the batts yet? have you equalized them yet? i know, dumb questions, but worth asking. i'd boil the snot out of them for 3-5 hours, and see how they respond. obviously monitering water level throughout. depending on the genset charging set up, they may have never been equalized.
and, to answer the question, i'm sure you'd be fine with eight of the smaller batteries... just buy some solar, you'd be glad you did!
adam