Regarding the flagellum and the type III secretory system homology, my views on what it does and does not prove are here:
Evolution of flagella - Wikipedia
...there are two arguments:
1) The flagellum descended from a basically modern type III secretion system
2) The existence of the T3SS greatly weakens the argument for ID based on the theoretical ICness of the flagellum, and makes the hypothesis of an ancestral T3SS-like system ancestral to the flagellum a plausible idea (strengthened by various other points listed in the article).
#1 is not supported by available data, #2 is, and they should not be confused although IDists usually argue against point #1 while failing to deal with point #2.
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