…sorry for being late to the thread. I just read through it and don’t have much to add from what has been said.
It sounds like you have already established that the watch is not stolen and that manufacture warranty will cover you. Condition is satisfactory. Those are the most important points.
Regarding the missing items. The cloth. I’m sure they will give you one for free when you visit a boutique. The USB only holds a copy of the instructions manual that you have received in print. You Can download that exact file from the webpage. I don’t see any value in that. I also have the suspicion that this is an older production date due to the box (which is correct) and the printed manual. A Journe boutique will be able to provide you with the production year if you have the serial number.