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"What's your source for the number of witnesses (38) who saw an object rising from the horizon and striking the aircraft? That number appears to be low based on the material I've read."

The same source that all the actual witness data comes from. The 736 witness accounts originally gathered by the FBI and published in PDF format on the NTSB website. I know that "hundreds of witnesses observed a missile streaking toward TWA 800" is one of the most commonly used phrases on conspiracy sites everywhere, but nobody has any data to back it up. Including the sites that use it.

I think part of your problem is that you're starting your analysis with the assumption that there could not have been a cover-up of a missile shootdown. Then, based on that assumption, you trust all the information provided by the NTSB, FBI, and CIA. Based on that information, which could have been laundered and fabricated in a cover-up, you arrive at the same conclusions as the NTSB.

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.