Can you compile a simple program like just:

#include <stdio.h>
int main(int argc, char *argv[])
{
   printf("hello world\n");
   return 0;
}

with your cross-compile tools?

When building GCC, you can hardcode where are the libc headers and other stuff. You may check that every path are correct with "gcc -print-search-dirs" and "gcc -dumpspecs".

In case you have problem compiling a basic program, i suggest that you strace gcc... you will see where it looks for which files and then fix the path.

$ strace -F gcc -o test test.c

(-F used to follow the subprocess like ld, etc)