I attended a five day Intelligent Design conference to see if it really was 'religion masquerading as science'. I was impressed with the level of scientific evidence supporting ID.
It is something of a shame you couldn't give us more information on this or on the details of the conference you attended, especially since several things in the rest of your post seems to substantially support the idea that it is 'religion masquerading as science', e.g. "ID is a champion for God".
It is car crash evolution - a car goes through a bush, hits a tree and ends up in a lake - the bush, the tree and the lake are objects of Nature but the car crash is not a natural process.
I think you need to explain in greater detail what point you are trying to make here. What is the unnatural 'car crash' part of evolution? Is it mutation? In what way is it unnatural?
While were at it, in what way is a car crash not natural? You seem to be trying to conflate natural with some sort of purposive teleological concept. Why are random events and accidents not natural by your definition? Is a coin toss unnatural because I can't predict its outcome?
Science, medicine, engineering are only possible because of the intelligibility, predictability and logic of Nature.
So why do you not accept that it is this same intelligibility, predictability and logic that have led to the conclusions you seem to disapprove of, dismiss as naturalism and claim have nothing to do with nature? Volcanoes do erupt, meteors do rain down and mutations do occur; do you think they don't?
This is why relatively long-lived species like reptiles, birds and mammals take at least 10's of thousands of years to form new species, while short-lived species like bacteria that reproduce several times per hour can form new species in very short periods of time,
You can't really meaningfully compare the two, a bacterial species is defined completely differently to what the Biological Species Concept would lead us to consider a species.
I'd also question your contention that long lived metazoans require 10s of thousands of years to produce new species because they have long generation times. Post-zygotic reproductive isolation can be established by changes in only 1 or 2 genes so there is no reason why it would take more than a few mutations to establish the necessary genetic variation for reproductive isolation. I'd suggest that the relevant issue is not so much generation time as population size, gene flow and genetic recombination/reassortment as a result of sexual reproduction.
So I disagree both on the time scale and the purported explanation for it.