"You'd also have to assume that this same 'blind' process happened not only once, but twice. That might sound reasonable to you, but it doesn't to me."
Argument from personal incredulity.
"If you extend your claims to saying that a non-intelligent 'something' (in this case 'natural selection') caused this design to happen not only once, but twice, then chance is indeed part of the discussion."
Obviously the bones were present in reptiles since they had a multiboned jaw, the genetics were predisposed to do this since it already happened once and better hearing is a survival adaptation, there is not much of a stretch. So it is not all chance. However, I am not too sure yet about this particular finding. It may be that there are still some fossils to be found that might clear some of this up and that this branch of monotremes came from the node of common inheritance with mammals with 3 bones in the ear.
You must understand the basis for evolution, the science behind it and the obvious fact that there is some structure to the molecules. I don't discount the fact that God could have designed the Periodic Chart, but He did not create each life form separately and probably didn't directly create first life. Just by "let there be light" an omnipotent God could have created everything through coversion of energy to matter.
As to the rest of your post, I'm glad to see you are open to God being the 'uncaused cause' for life.