I see no massive issue with a fan on the GPU card, but you might find that adding case fans screws up the 'airflow zones' inside the case. You might be better off trying to replace the fans that are already there if possible.
Loc: Florida, USA
I try to avoid the molex Y cables and fan adapters. I would splice into the main power source say from the hard drive, just splice it into the molex connector going to the drive. That way you only have two wires to deal with instead of trying to stuff a adapter in.
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