I don't know what you're talking about here. Besides, Archie isn't really being proposed as a true transition between dinosaurs and birds. It's on kind of a side branch that seems to have died out. It's primary importance is proving that such a transition is clearly plausible because of it's incredible combination of dinosaur and bird features. It's just not close enough to be a true ancestor of modern birds.
http://www.talkorigins.org/faqs/archaeopteryx/info.html#ancestry
As to the ragwort thing, check out my response to Halffull about the difficulties in drawing classification lines. Are hybrids new species? Were their 'parents' seperate species to begin with?
After disecting that enigmatic quote from Dr. Shapiro, I'd say he was accepting evolution in principle, but reconciled it with his faith by supposing the hand of a creator in subtly influencing events. (Please correct me if that's not correct, I had to infer a lot) As this position contradicts none of the evidence you've been arguing with me about, I would say that this is perfectly workable. What's the problem with evolution? What does it contradict in your faith that makes it so impossible to reconcile the two?
Dr. Shapiro has made no statement, of which I am aware, of his faith. He doubts what you appear to embrace, Darwinian or Neo-Darwinian theories of evolution. He has not expressed his view of ID, but the quote was from a discussion on "International Society for Complexity, Information, and Design". This group includes William Dembski and Michael Behe which will hurt Dr. Shapiro in the eyes of Darwininians.
The Archie is older than the Sino by about 15 million years. Plants hybridize. Animals hybridize. Are the hybrids new species? If they are does that demonstrate evolution? Is the camel/llama hybrid a new species?