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Re: where have all the etc.[Pharris]

With dozens to choose from, some disagreeing with others, some not
including taxa that others do, which character list shall we start with?

All, of course. Grab all characters you can find. Where two papers disagree on which character state a given taxon has, check which is correct. If you can't check that (because the text and the illustrations are too imprecise and you haven't seen the fossil itself), then you have four possibilities -- code it as "?" which is probably wrong, drop the taxon, drop the character, or be _VERY_ cautious about the results of your analysis (for example, try what changes if you drop the taxon or the character).
That's one more reason why I don't trust my bird analysis too much -- even though it has more taxa than any published one and includes some corrected codings that haven't made it to published analyses yet. With the exception of some 2 or 3 entries, all my codings are from the literature, most of which is rather superficial.

Extraordinary claims? Hardly. You should know that this study repeats
the results of earlier work whenever similar taxa are employed.

Even the destruction of everything that resembles Archosauria?

Often the introduction of novel taxa takes the form of using species or
specimens rather than a priori suprageneric taxa.

Which reminds me: how much do you attempt to correct for ontogeny? A recent study on the phylogenetic placements of the neotenous salamanders is entitled "Ontogeny discombobulates phylogeny: [...]".

Case in point: The only time (tell me if I'm wrong) that lizards and
pteros both appeared together in a cladogram (Benton 1985) they showed
up as sister taxa.

The big analysis in Senter's thesis has lizards and pterosaurs in their usual places, I hear.