Pin Naming

That won't actually change the pin names though. This is one of the problem with schematics, as a lot of the cutting and pasting things just don't work. You will have to hand-enter them. You could also try VHDL/Verilog. Take your .bdf and go to File -> Create HDL File for Current File. Then you can edit the HDL. (It's still going to take some manipulation, but text manipulation is generally much easier.) Note that you won't be able to convert it back though, i.e. you're committing to learning HDL, which isn't a bad thing.