The fuel petcock may be the problem. It works by opening a valve to let gas reach the carbs. It does this using a vacuum diaphragm drawing vacuum from the carbs. A gs500 will not work very well without an airfilter either. The carbs rely on proper vacuum to operate and a poor or no air filter will make a gs500 run very bad. Gs500s are air cooled also. If none of this solves the problem do a major tune up. Still nothing then take it to a mechanic. Taking shots in the dark gets expensive.
Remove carbs and clean real good also tank you might have some water in tank or debris in carb's
Sounds like it could be overheating. Is there any coolant in the radiator?
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Same thing is happening to mine one, a 07 GS500. Did you manage to solve the problem?
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