It doesn't strike me as a big deal that the boxes were moved in the search for evidence and perhaps no one remembered exactly how they were found. Again, not ideal but so what? Oswald's rifle was found. Fired bullet casings from that rifle were found. His prints are on all the relevant evidence. After nearly 60 years of every official investigation and many "researchers" looking under every rock, there is still no credible evidence of the involvement of anyone other than Oswald. There are some folks who would not accept that Oswald was the assassin even if they had a time machine.
Just because we can never know everything with absolute certainty doesn't mean we can't know anything or reach reasonable conclusions about what happened. That is the basic distinction between LNers and CTers. CTers are unable to distinguish information from knowledge. They become overwhelmed by endless details. They see anomalies or unimportant details that can't be exlained to their satisfaction as de facto proof of conspiracy. The conclusion or implications they draw from this information doesn't have to add up to any coherent counter narrative or even be mutually consistent. They can draw inconsistent conclusions from the evidence and not miss a beat (e.g. the purpose of the conspirators was to start a war with Cuba but the conspirators framed Oswald and ignored evidence of Cuban involvement). Until someone can explain the presence of Oswald's rifle on the 6th floor and why Oswald lied to the DPD about his ownership of that rifle, there is no real uncertainty about the only issue that really matters. Who killed JFK? The evidence confirms that is LHO even if we can't answer every question about that day with certainty.
"The conclusion or implications they draw from this information doesn't have to add up to any coherent counter narrative or even be mutually consistent"It is surely time for a coherent counter-narrative to be produced that (non-mental) CTers can get behind as there are aspects of this case that do not sit well with the LN narrative (nearly everyone who was on the 6th floor lying in their various statements, the Rose Cherami case, Shelley in New Orleans etc.)
Until then it's just endless rabbit-hole

I disagree about the importance of having two completely different photos of the crime scene in evidence and just repeating "Oswald's rifle" isn't addressing the issues being raised in this thread. I get the impression, because of the bitterness generated by the fringe (see Otto's post above), you can't engage in any sensible discussion about the incompetence/corruption of the investigation without half a dozen arseholes jumping down your throat.
It's all really f^*king annoying.
Other than the points raised in this post, it is very difficult to argue with anything you're saying.