Jon writes:
Is proper science about the methodology used and not the source of the inputs?
Absolutely.
Jon writes:
Does use of the Bible and other histories represent an appropriate application of these methodologies?
It depends on how you use them. The explanations provided in the Bible and other histories can be considered to be theories explaining why the universe operates the way it does. Those theories can be tested in exactly the same manner as theories concocted today by scientists.
As for the accounts of events being considered data, thats a much more tenuous prospect. Most of these accounts are quite unreliable from a factual standpoint; there simply isn't any reason to be confident that Jesus actually came back to life after 3 days of being dead for instance.
Jon writes:
How can we address the implications of these two points as they relate to our understanding of the conclusions derived from the different inputs, that is, if use of the Bible is properly scientific, then why is it 'wrong' and what/who is the cause of its 'wrongness'?
The Bible isn't "scientific", mainly because that term doesn't properly apply to such a record. The Bible is "wrong" in the sense that it is an unreliable account of historical events. To be sure there are *some* agreements with accepted history but it deviates significantly overall. This assessment is backed up with hard data; there simply wasn't a global flood as claimed in the Bible. Period.
The Bible should be approached from the same standpoint of recovered lab notes from an alchemist 800 years ago which tell of an experiment which successfully changed lead into gold through the combination of lead with powdered unicorn horn, heated with dragon's fire.
The claim and theory can be taken at face value, but the recorded data of the experiment is unreliable. Current tests and competing theories soundly trounce the alchemist's theory, so we should dismiss the claim and ignore the data.