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It looks as though changing PyLong_SHIFT to 30 everywhere is much simpler 
than I feared. Here's a short patch that does exactly that. It:
 - changes the definitions in longintrepr.h
 - changes marshal.c to write digits as longs, not shorts
 - adds some casts to longobject.c (most of which should really
 have been there already---clearly Python's never encountered
 a machine where ints are only 2 bytes long, even though the
 standard seems to permit it).
With this patch, all tests pass on my machine with the exception of
the getsizeof tests in test_sys; and sys.getsizeof is working fine---it's 
the tests that need to be changed.
Still to do:
 - use uint64 and uint32 instead of unsigned long long and unsigned long,
 when available; this avoids wasting lots of space on platforms
 where a long is 64 bits.
 - provide fallback definitions for platforms that don't have any 64-bit
 type available
 - (?)expose the value of PyLong_SHIFT to Python somewhere (in sys?); then
 the getsizeof tests could use this value to determine whether a digit
 is expected to take 2 bytes or 4 (or ...)