[tex-live] installing with custom binaries & making it

[Karl Berry]

    Where in makefiles (or anywhere else) is texlinks invoke string? 

Gee, I already gave you this information -- the top-level
source/Makefile[.am] is what invokes run_texlinks.  Apparently you did
not actually look at that file, which says:

texlinks_dir = texk/texlive/tl_scripts
world: all
..
	@echo "top-level make $@: running texlinks in $(texlinks_dir) ..."
	cd $(texlinks_dir) && $(MAKE) $(AM_MAKEFLAGS) run-texlinks

So, the directory is source/texk/texlive/tl_scripts.

    Where is this 856th line actualy?

Of course the generated Makefile with the "856th line" is under the
build directory (.../Work).  The original Makefile.am is usually easier
to look at.  Anyway, both contain:
..
run_texlinks = $(DESTDIR)$(bindir)/texlinks -v \
..

Thus, from your output, evidently $(DESTDIR)$(bindir) is expanding to
the incorrect /bin/x86_64-linux, instead of your stated --bindir.
I cannot say why.  Maybe you ran configure more than once, or have
environment variables set?  I'm just guessing.  Only you can determine
the facts of your environment and configuration.

    Should I manualy edit it some something else?

If you just want to get on with life, it appears to me that you could
edit the above line in Work/texk/texlive/tl_scripts/Makefile to say:

run_texlinks = texlinks -v \

Since according to your output, you already have the right
/.../bin/custom directory in PATH, so it should be found that way.
Whether there would be subsequent problems due to the misconfiguration, 
I cannot guess.  Wouldn't surprise me either way.

hope this helps,
karl