> Note that when I run into build problems after an update, I generally
> run 'make distclean' and then redo the configure/make.

Yes, but I believe that won't help with changed Modules/Setup* files and, because it is needed in the core interpreter executable, timemodule.c is supposed to be built using Setup and not setup.py.  Setup and Setup.local are designed to be locally modified and thus not revision controlled nor cleaned by make clean:

$ cat Modules/Setup.dist
# The file Setup is used by the makesetup script to construct the files
# Makefile and config.c, from Makefile.pre and config.c.in,
# respectively.  The file Setup itself is initially copied from
# Setup.dist; once it exists it will not be overwritten, so you can edit
# Setup to your heart's content.  Note that Makefile.pre is created
# from Makefile.pre.in by the toplevel configure script.
[...]
$ hg stat --all Modules
I Modules/Setup
I Modules/Setup.config
I Modules/Setup.local