Caffeine has nothing to do with it as far as I can tell and seems to be associated with all the negative health aspects.
Again that is your belief. The research that I have cited uses caffeinated coffee. You seem to be starting with the assumption that caffeine is bad and looking at the research through that perception. That is not a good way to look at research.
In my opinion, isolate whatever is good from coffee, separate it from the caffeine in the lab, and then sell the product in a pill. Then do a long term study which compares the pill takers to the coffee drinkers to see which group gets the most health benefits.
Again I think you fail to understand how medical research is done. This kind of study would be ripped to pieces for poor methodology as taking a pill is quite different from drinking coffee. How would you know before the study what components to keep and what not to keep? How would the bioavailability and stability of the components compare when using an aqueous solution verses a pill?
It would be better to compare identical types of coffee except for the caffeine in order to do this. In that case you would need to ensure that the caffeine removal process did not change anything else about the coffee.