How to make the gcc source files for nios2 cpu

I'm a little confused by your question. I don't see why changing the board would mean you have to change the compiler. You would only need to modify the compiler if you were changing the processor.

You can modify the compiler to change the linker defaults, but all these options can either be changed at the command line or in a linker script.

The only documents for how to build the compiler are the Gnu documents and we would very much advise you against doing this, unless you've done it before.