Eli, you mentioned 'transcript', is it the following?
---8<-------------------------------------------------------------------->8---
address@hidden emacs]$ make bootstrap
Yes, thanks.
`/bin/pwd`/temacs --batch --load loadup bootstrap
Loading loadup.el (source)...
Using load-path (/src/opensource/emacs/lisp
/src/opensource/emacs/lisp/emacs-lisp
/src/opensource/emacs/lisp/language
/src/opensource/emacs/lisp/international
/src/opensource/emacs/lisp/textmodes)
Loading emacs-lisp/byte-run (source)...
Loading emacs-lisp/backquote (source)...
Loading subr (source)...
Loading version.el (source)...
Loading widget (source)...
Loading custom (source)...
Loading emacs-lisp/map-ynp (source)...
Loading env (source)...
Loading cus-start (source)...
Loading international/mule (source)...
Loading international/mule-conf.el (source)...
mv -f emacs.exe bootstrap-emacs.exe
mv: cannot stat `emacs.exe': No such file or directory
This shows the problem very clearly: for some reason, the command that
should have produced emacs.exe didn't run to completion, but rather
finished prematurely (a.k.a. crashed) after loading only a handful of
*.el files, the last one being mule-conf.el.
The Cygwin build of Emacs is currently very troubled. In particular,
only a few versions of GCC are known to produce a working binary.
Please see the entry in etc/PROBLEMS whose header is "Building the
Cygwin port for MS-Windows can fail with some GCC version". Also, you
will find a few discussions in the archives of this list about similar
problems that might help you find a solution.