How long did it run well? Here are some things you should know:
The float valves in the carbs should have prevented this if they were working perfectly.
it is possible for foreign material to enter carbs which are clean, if there is foreign material like rust in the fuel tank. This is pretty common when bikes don't get used. I once cleaned the carb on an old rotary valve 100 single for a guy running an RV Park I stopped at. His kid had a blast riding it all over the park for about 20 minutes, and it quit. I pulled the filter bowl off of the petcock and it was packed with rust.
You really need to have a look at precisely what you are dealing with here.
On another note, I just got my 1978 GS1000E going this week for the first time in over a year. The carbs had been drained for storage. The two inside carbs leaked through the overflow tubes. I rapped on them a couple times with the handle of a screw driver. This will often correct a stuck float. In this case it did not work. I ended up draining those two carbs twice each, which apparently flushed out whatever was hanging up the float or needle valve. They are not leaking now.
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