I have the same problem, but even doing this linking, it isn't fixed.
It still says the same

Your Linux kernel header files cause errors when included by a C++ program.

Click modifies the Linux kernel's header files to make them work with
C++, using the program 'linuxmodule/fixincludes.pl'. It looks like
your kernel header files have features that 'linuxmodule/fixincludes.pl'
doesn't know how to fix. You can report this error to us on the Click
mailing list, or, even better, try to fix the error. See the config.log
file for more information on the error.

Ubuntu has only linux-headers-3.16.0-30-generic folder with no arch-specific folder.

from click.

Did you also merged the headers-common with headers-amd64 (or other arch-specific folder) before the ln -s autoconf.h ?

mkdir /usr/src/linux-headers-merged/
cp -r /usr/src/linux-headers--common/ /usr/src/linux-headers-merged/
cp -r /usr/src/linux-headers--amd64/ /usr/src/linux-headers-merged/
then the ln -s.
And use the linux-headers-merged as the --with-linux path

I also have a problem which appeared recently with proclikefs during make, solved by doing :
sed -i 's/d_u.d_child/d_child/' linuxmodule/proclikefs.c
And have another make error corrected by adding this line in include/click-linuxmodule/include0/asm/barrier.h :
#define alternative(oldinstr, newinstr, feature)
asm volatile (ALTERNATIVE(oldinstr, newinstr, feature) : : : "memory");

from click.

@yahyaezzeldin I come into the same problem, do you fix it now?

from click.