S-parameter bi-section for deembedding
To answer (1), I would recommend de-embedding differently, namely "gating".  Gating is done in the time domain.  Most VNAs will gave a time gating option.  The same holds true about noise and large impedance mismatches, but you should be ok here.  For a really good paper on gating, read Joel Dunsmore http://ieeexplore.ieee.org/xpl/login.jsp?tp=&amp;arnumber=4804303&amp;url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F4801867%2F4804274%2F04804303.pdf%3Farnumber%3D4804303

EDIT:  I'll add a link to a short paper I wrote a few years ago that basically sums up the Dunsmore paper with examples time-domain gating