Wow. Is there any aspect of President Kennedy's presidency that is NOT shrouded in mystery, or conspiracy?
So, in light of this new evidence, the real question that needs to be answered without a doubt is what was the VIN/serial number of the actual car that transported Kennedy? All we really know for sure is the number on the door.
It seems more likely that the one pictured in the junkyard is the one, but it is still possible that the library received a car that was thought to be the correct one, but wasn't (if the documents presented by BJ are correct and authentic). If they are fakes, then someone is pulling a very convincing fast one. Unless I am missing a bit of information somewhere that ties all these identification numbers together that is not under dispute, about the only way to possibly resolve the issue is to start involving experts at dating documents, paper, ink, typewriters and handwriting to verify the validity of the documents that have been presented. There are experts that could tell if the BJ documents are fake or not by dating the materials involved, but I'm not sure anyone is going to go that far.
At the very least the car should be pulled from auction pending further investigation.