1999 and 2000 Busas are prone to this because of the fuel pump design. What you see as rust in the filters is actually part of the fuel pump impeller that rubs inside the fuel pump housing. As long as you use a 99 or 2000 Fuel pump you will continue that have the clogging problem over a period of time. I would suggest going to an aftermarket fuel pump and fuel pressure regulator. Once this is done you can install 2 fuel filters (one before the pump and one after the pump) this is eliminate the problem. Then pull the screens from the injectors.
RC Engineering does a great job of cleaning and balancing injectors.
RC Fuel Injection
MPS Racing can clean them but not balance them
cost is about $100 to clean them