I don't claim to understand how the charging system works as a whole, but if you're handy with a meter you can try some of the component tests described and/or linked to in the old thread Charging system (http://www.gstwins.com/forum/viewtopic.php?t=4770).
You might also try some searches for words like "rectifier", "regulator" and "stator".
I'd check for corroded or loose battery terminals and connectors first. Then, I'd take a long hard look at the battery. Has the water level been maintained (with distilled, hopefully)? Two years is about when battery troubles begin. You can buy a inexpensive battery tester (with the little colored balls inside the tube) for a coupla bucks.
The direct replacement battery for a GS (YB10L-B2) is often pricey; if you're willing to reroute the vent hose from the right side to the left (while still having it drain on the right-- important!), you can buy one with the same capacity (YB10L-A2) for about $30.00 at Walmart.
buy a cheap digital voltage meter...radio shack $5-10 bucks
before starting the bike test voltage of the battery...should be 12.5-12.9 volts
leave seat off
start bike and check voltage....should be 13.5-14.5 volts
when you rev the engine...volts should go up a little
the battery condition.... sounds like its time for a new one.
and remember jump start with a car....do NOT start the car!!!!!!!
it will blow the volt regulator
hope this helps