Even if the compressor has not failed,,, if the system is open it is a good idea to flush
(((( and it has not been mentioned lately .but the standard operating procedure is that if the system is opened up then you replace the reciever dryer.. it is cheap insurance, like good oil changed often for the engine...))))
... because the other major thing which can put JUNK into the innards of the system is the Reciever/Dryer... it has a bag of Dessicant... and some are made from a cloth like material.. so if that gives way.. from old age/ acids / vibration... then that stuff is in the system...
It is also good to install the filter Larry mentioned....

Oil is in the compressor (casing?) ... but the top end of the compressor is lubricated by the mix of oil moved through the system by the refrigerant...

So even if you have oil in the compressor... but did not have enough refrigerant to move oil around , after sitting for years, to lube the top end it is possible the noise is from that...

But if there is enough to move it (oil) around.. after a few minutes of running it should not be making any clattering sounds (due to having sat for years)... But check to see if it could be the clutch making the sounds... a good stethescope helps on some things like this...