Is there a chance that this unit has a schematic attached inside that you could scan and post? It would be much more helpful to see how it is already setup.
As ante has mentioned, there are too many parameters to be able to give a "one size fits all" type of answer.
I know this is an older post, but I have a lot of UPS experience.
It sounds like you found an old Emerson UPS with bad batteries. Most likely there is only a few bad batteries in the string so you wont need to replace all of the batteries.
What you need to do is get a constant current supply and inject each battery block with 10A of current. With a DMM measure the voltage across each cell. You should get a voltage in the 80-150 mv range. If the drop is above 1V there is an open cell and you need to replace that block.
Since all of the batteries are in series they all need to be functional for the string to operate.
As far as the generator is concerned, are you trying to use a DC generator to power the DC bridge? Or using a transfer switch have a standby AC generator.
I guess it doesn't matter because neither will work.
DC Generator: If you use a DC generator to feed the DC Link during a power failure, what is going to turn the generator? The Power is off, that's why you bought a UPS. I can think of at least 3 more major problems this would cause.
AC Generator: This wont work without batteries either. The function of the batteries is to bridge the gap between the beginning of the power failure and the time it takes the generator to ramp up to full voltage.
If you want your UPS to work, you are going to have to invest in the new batteries.