you likely have power factor issues with your charger which makes the genset work far harder to deliver what is needed
for instance you want 40amps a 48 volts (lets call it 50volts for easy math) so
40*50 = 2000 watts at unity power factor
my bet is your power factor is probably miserable so you need to generate maybe 3000 watts or more to deliver 2000 watts
then if you factor in efficiency losses you might need to generate close to 4 kwatts to get 2 kwatts charging, and then you are quite overloaded.
to answer your second question
i am not aware of an autmotive alternator that is cheap that can be used out of the box to charge 48 volts, but
there are a number of ways to do so.
a. go to electrodyne and spend big bucks for a 48 volt alternator, or
b. use a 12 volt alternator and some switch gear to charge your battery bank in sections, not a pleasant option but can be done
c. do the same with a 24 volt alternator, or
d. build a custom regulator to control either a 12 or 24 volt alternator so that it can deliver a controlled charge into a 48 volt bank, the alternator
will have to spin faster to do so but it can be done fairly easily.
e. have an alternator rewound to 48 volts, tedious if you do it yourself, or expensive if you have someone else do it.
f. reconnect an automotive alternator stator from the typical delta to wye configuration and then you can use option (d) at a lower rpm.
g. get an st head and reconnect the stator poles via relays so that each pole can be parallel connected which will get you to approx 60volts
but you will need a purpose built regulator to control it as well as a rectifier back to get it to DC for charging.
just a few of my favorite things,,, lalala
anyway, i don't believe you have a problem with the SOM, but you likely have efficiency and power factor issues with the charger both of which
will make it nearly impossible to get anywhere near 40amps charging into your 48 volt bank. 20-25 amps is probably more the reality with that setup.
i am relatively certain that you could do much better with an automotive alternator and a purpose built regulator, and maybe reconnect the stator
from delta to wye if necessary to keep the rpm down to a reasonably attainable range. you might have to go upwards of 6k rpm unmodified, and likely be around
3.5k rpm if reconnect stator to wye.
if you are going to go this route, then step up to a heavy duty truck alternator such as a leece neville or prestolite, an try to find one that is 24 volt to start with
that way the rectifier bridge is likely high enough in PIV rating to handle the 48 volt charging without burnout,,, even if that became an issue the leece nevilles and prestolite alternators have external stator leads that you could remote mount a rectifier bridge to if you found the need for doing so.
bob g