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Michael, I'm not sure I understand the issues in detail,
however I will try to respond.  signed/unsigned issues are
probably used and checked inconsitently--be wary of them. 
There are potential issues when the high bit is set and
whether that means a long or unsigned value.  The meaning
has changed in some versions of python.

I would definitely like to see shadowed variables fixed.

If you don't believe a comment is correct, you should fix
the problem whatever it is.  So fix the comment and/or code
as you see fit.

If the patch gets too large, feel free to break it up into
several related components if that makes sense.

I'm just starting to read over your analysis.  Thanks for
looking into these issues.