You are a treasure trove of info when it comes to supplying sources! As Dodie says, seeing it all together is baffling and amazing all at the same time.
Now, lets see if this sequence makes any sense to anyone:
French goes through first. No report that he notices the broken window or a chair in front of the door of the train room. If he went into the train room, he would have had to move the chair. It's possible he (and maybe the other officers either missed the broken window or didn't include it in their report? Only very slightly, but still possible. A simple statement of "no sign of forcible entry" could have also meant they assumed the break was old, and the window closed, under the grate with webs would have supported that.
Fleet goes next. Notices the closed, but unlatched broken window. And said he moved a suitcase around and put some glass he found on the ledge.
John's turn. He goes down, has to move a chair to get into the train room. So, did Fleet place the chair in front of the room as he exited? It would seem so, but why?
If Fleet moved the suitcase around, Fleet could have placed it under the window, where John said he saw it. John said the window was standing open about an inch. If Fleet noticed it was unlatched, and the train room door had then been closed and reopened again by John, is it possible there could have been enough of a suction created to pull the window open a bit, as John said he found it? Then he could have closed and latched the window, as it was when he and Fleet went back in together later.
First John claimed this trip of his to be early, but from the above timeline, the time would have had to be between 6:45 (after Fleet got done) or so and 7, since he was on hand for officer arrivals and again at 7 when going up to Burke with Fleet. Here is where I think this is a lie. I do not think John was down there after the police arrived, until he slipped away from Arndt's watch after the 10 am deadline passed.
Now, let's think about John saying he had 'found' JB, and didn't want Patsy to see her that way, so he went up near the TV room, got a blanket and covered JB. If this is at the same time he also went into the train room (had to move the chair - during his trip when missing from Arndt), it's possible he bolted back up and grabbed the blanket from near the TV room without anyone seeing him, hustled back downstairs with it, to provide extra coverage of JB's body. There WAS an additional blanket found (plaid, IIRC) in the WC, other than the white one JB was wrapped in.
Fleet said when he went down at 6:30, he looked into the WC and saw nothing. Notice, John does not say where he 'found' JB, just before he got the blanket that he placed over her to keep Patsy from seeing her. It has been discussed many times that her livor pattern said she would have had to be in the same position, but that it was possible she could have been moved a short distance by pulling her. Since she was wrapped in the white blanket, and it was under her, (fibers were collected from it later), wouldn't it be possible she could have been pulled out of the deep corner to the left of the door inside the WC by tugging on an edge of that white blanket, OR even by pulling that cord that was between her wrists, or worse yet, the 'stick' handle? She might have even been lying on the piece of sheet metal that was taken into evidence later by the police, which would have acted as 'sled' in moving her. The blanket taken from near the TV room could have then been placed over her body (or also used while pulling her), and tossed aside when John went down later with Fleet and really "found" her. She could have been moved from the corner of the WC during this visit after 10 am, to where she was later "found" with Fleet after 1 pm.
This would have coincided with what JR told Long and JAR on the way to Fernies later, which he said was about 11 am. If JR would have had to pin JB's death on anyone as "an inside job", he would have wanted to establish that he "found" her at that time, which might have explained why they didn't get the ransom call they were expecting. And would also have made his family believe the reason he didn't bring her up then was because he was going to wait for the call that should then come the next day, so he could go ahead with the ransom note instructions (except the 'kidnappers' would have killed JB) and he would be the hero to his family that got Patsy or Burke off the hook, if necessary.
Did John go down after 10 am, just to make sure the broken window could get noticed later by someone to be considered a possible point of entry/exit? Even though he said he would not have put the suitcase in that room when he took it to the basement, I think he wanted that suitcase placed so it looked like help for an exit. I believe he lied in saying he put that suitcase elsewhere, and instead had taken it specifically, from where he had found it earlier, to that room to be used just as it was. That is when he finalized the 'staged intruder kidnapper' theory that was originally intended to be used.
He said he told Arndt about the window when he came up then. He hoped he'd plant the kidnapper entry/exit point, which occurred to him because he had gone back down to check for that, and then saw the window he broke last summer. But Arndt wasn't buying it. Her experience had already raised her hackles about JR. He was reported to have been acting very disturbed from that time on. Because she didn't react to his obvious lie?
The FBI had told the BPD investigators to look at the parents, and expect to find the body. Arndt dropped the bomb after the call did not come in when she told John to take someone and search again. John HAD to find JB this time, because either Fernie or White would have insisted they check the WC again in a team search. Fernie went off by himself upstairs, so JR had luck on his side to take Fleet immediately to the train room, where he again tried to establish the kidnapper entry/exit by pointing out the window situation to Fleet. Even to the point of looking with Fleet for fresh glass shards. Then, he knew he'd have to get into the WC and 'find' her, so he could contaminate the scene, her clothing and body, since it would now be impossible to wait things out and remove her from the house at a later time.
I think Patsy told the truth when she said her voice was kinda cracking and she remembered screaming for John, remembered him screaming as he came from the basement. I think she did hear him scream, possibly back at her, as he bolted out of the basement earlier that morning after first being with JonBenet in the WC. If the train room window was broken that morning and the glass cleaned up, it was before JR was in the WC with JB.
At this point, we still don't know who was the one most likely to have hidden JB in the far corner of the WC.