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Ah, that storage box.
I'm not sure of the circuit for the brake handle, but if the box sometimes doesnt close properly, theres probably a problem with the latch mechanism, which ties to the security system (makes the horn honk when you lock the car if the lid isnt closed), so MAYBE it could affect the top operation, but thats a long shot.
You will have to take the center console off to troubleshoot it though, and you can check out the wires. They could be shorting, causing other weird problems with the alarm system/top.
Since so many random things are happening, it could also be the ignition switch, which isnt hard or expensive to replace
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