Again, you are confusing issues. Your original claim was:
"Because if God did everything that we can't explain, then where's the motivation to find out what we don't know?"
You still did not support your claim of "everything". Behe's criticism is not that evolution has not occurred -- in fact he specifically thinks it did. Instead, Behe's claim of Irreducible Complexity is that the Darwinian process is incapable of producing such structures, not that no theory of evolution can produce such structures. Behe's main point is that science is stuck defending a dead mechanism that has no explanatory power, and it should get off its duff and explore other options.
In addition to that, Irreducibly complex systems match very closely with what designers normally design. Therefore, looking for design in biology is a valid preliminary inference, precisely because Irreducible Complexity matches what we know about how designers do design.
"The research on flagellum evolution has since explained away Behe's argument"
(1) Making up stories is not equivalent to an explanation. (2) Saying the small parts have other uses is likewise not an explanation, just as having a screw being part of a computer does not mean that a computer evolved from screws.
"but like typical ideologues, the ID and creationism advocates don't recognize that they've lost that fight"
If scientists can show experimentally how the flagellum developed, then you can call the case closed. Or, instead, show mathematically how such a feature is likely.
"Behe was satisfied that he had the answer, based on a lack of knowledge. That provides motivation to halt further science."
No, it halted further exploration of a Darwinian mechanism. It did not halt inquiry altogether. I'm all for abandoning dead theories. I don't think we should stick to bad theories just because someone will think that I'm "halting progress" on it. Bad theories should be halted, and replaced by better ones.
You seem to be arguing against design a priori as a bad argument for anything. Does design exist at all? If not, then we should fire our artists and programmers and just write a master program to do it. If it does, then you are excluding an entire mode of operation that is EXTREMELY COMMON in everyday life simply because of personal preference.
"Very true. But religion has abandoned acceptance of most of science"
Most of science? Are you serious? Please name the scientific law that Churches are explicitly against that is experimentally verifiable. (note that I indicated "law" because laws are mathematical, thus eliminating both fudge factors and speculation).
"My particular theory is that faith has acted as a filter, dividing people between those who can understand abstract logic, vs. those who operate emotionally."
This ultimately gives you away -- abstract logic can only lead from premises to conclusions. It appears that it is you who do not understand abstract logic. My favorite Star-Trek quote is, "logic is the beginning of wisdom, not the end of it". Abstract logic only works if you have correct assumptions, but logic cannot tell you whether or not your assumptions are correct. If you have bad assumptions, logic will lead you the wrong way. My own theory is that Darwinists are people who _only_ have abstract logic, and not any other facet of wisdom. Therefore, they are unable to analyze their own assumptions, because logic is their only tool, which is completely inadequate to the task. It is true that there are some in the Church without logic, but I think you are confusing what you see as a "lack of logic" with what is really a "broader wisdom than logic alone can provide".
Deductive logic, which is what you are referring to, is a very minor tool with minor applications in science, much like a microscope. Serious scientific reasoning, including about biological evolution, much like in any other serious human enterprise, is largely the domain of inductive and analogical reasoning.