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As on any vehicle, it's best but not absolutely necessary to remove the battery. If it has caps on the top (6ea), be sure they are all full to the marks on the case. Attach red-positive of the charger to the "+" on the battery, black-negative to the "-" (in a pinch to the frame or a bolt on the frame), your charger should show it's taking a charge. BE SAFE!!! Batteries emit combustible vapors while charging!!
Check your battery first, if it's more than 2 years old, it could be had it. Disconnect the battery, and check the voltage with a multimeter, if the reading from your battery alone, is less than 12V, then your battery is no good. To check your alternator function, using your existing battery, start the bike up, and check the voltage reading at idle, should be about 13 - 14Volts if your alternator is charging the battery.
Turn off ignition. Disconnect battery terminal leads, ensure fluid levels are ok, connect charger leads. It is best if you remove battery so you can give it a clean and save your bike if something is amiss somewhere and it erupts or leaks when charging. Try the sites below for manuals or go to Wiki Q & A under S40 Boulevard, then wade thru' for links.
Yepp, since you replaced the generator and you checked the cables, there cant be anything else, the battery is out of time and wont charge.
And its easy to check, take the bike to a repaire shop and let them measure the power your new generator gives, it takes 1 minit to check that and they wont charge you for it ( if they are nice guys ). But i will say that you need a new battery.