First thing is to check both brake switches. In your work on the bike you may have, for example, bumped the hand protectors. On on '05 GS if the hand protector is rotated slightly it will push the hand lever in just enough to toggle the brake switch, causing the problem you are experiencing.
Once you've made sure that the hand guards aren't touching your brake or clutch lever check the switches by gently moving the lever with the ignition off while listening very carefully. You should hear the click of the switch on both the hand and foot lever.
Let us know what you find out.
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