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Nice results, great work.  My humble opinion on this is that all known instances should be fixed.

The type size_t could be an int or a long depending on compiler/platform (or maybe even something else), so it should just not be used.  Any signed/unsigned conflict should also be investigated; most but not all seem harmless.

Of course, tests would be nice, but I don't completely see the point of spending too much efforts testing dark corners that we are pretty confident are getting fixed, when the code is under-tested to start with.

The Py_BuildValue() logs are more tedious to look through.  There are definitely some int-vs-long conflicts.  There are signed/unsigned conflicts, but some are intended, e.g. in binascii -- in these cases, though, an explicit cast would not hurt.

In any case if you embark on this clean-up, I volunteer to review and apply it (be sure to work on the subversion head).