Dude! Glad you found that noise.
Loose bolts on any rotating machinery bits bode no good. BTDT more than once in my life.
As for the wrench falling back in, I keep not one, but two of the telescoping magnets that fit into your shirt pocket protector when collapsed. Just in case I forget to put one back where they live on the side of the rollaround tool chest.
In addition I keep two pairs of forceps and two antique mechanical fingers in the bucket organizer of "ready tools" for most garage chores.
I also like your organizing your mods and stuff under one umbrella. I hadn't seen your pannier rack mods before, and like those. Keep it coming.