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 ...)