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.

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