I suggest starting with no assmption that there was not a cover-up. Then go to the raw data of eyewitnesses who were close to the accident scene. I'll take a look at this, but I'll bet that the 38 people who saw a missile or flare were closer than average to the accident site (that's why they saw it.) Also, look critically at the behavior of government agencies and do not assume they were not engaged in a cover-up. I'll take a longer look at this and get back to you. Based on what we know for sure, I don't think any theory can be ruled out. We can only assign probabilities to a few different explanations for this accident. I suggest that you not assume that material from government agencies is true, complete, and accurate.
You raise a valid point, so let me give you a little background. I hadn't thought much about TWA 800 a few years after it happened until I read a thread on this site posted by Micheal Rivero. In it, he claimed TWA 800 was shot down by the US Navy. Based on my experience, that didn't seem logical, so I started looking into the matter. I am a person who doesn't like to read other people's analysis if I can read source data on my own. So I did. Since the NTSB report is the source document in dispute, I read that first. All of it. Then I read information from various "independent research" sites. Time and again, I found them claiming the NTSB report said things it didn't say, or didn't say things that it did. And their information on things that I was an expert on, was typically way off. Five years later, I've heard and seen it all, and the conspiracy evidence just gets weaker and weaker.
I don't automatically assume material from government agencies is true. I really don't. But because of my background, I am a literal expert on much of what is bounced back and forth in conspiracy theories surrounding TWA 800. I have witnessed missile launches of all types from the air and ground. My life depended on knowing their capabilities. I know how they work, why they work and where they work. I've witnessed their effects. And when I read "proof" on conspiracy sites that runs counter to reality, it isn't hard to dismiss their theories.
As a commercial pilot, I have some insight into all the things that can go wrong on large, hardworking, commercial aircraft. I read about "one time" malfunctions all the time. Often times, "one time" means "the first time" as parts get older. On the airplane I currently fly, we have an entire section of our emergency procedures added as a result of data gathered during the TWA 800 incident. And again, when I read information on conspiracy sites that runs counter to reality I am living, it isn't hard to dismiss them