The spool pin will be easy to replace. I'm guessing it's a screw in - most of the Japanese machines I've worked on have had screw in, not tap ins. I think there are a couple of different sizes of thread - I had one machine I ordered the wrong pin for 3 times!
Now I write that stuff down! If the machine wasn't latched to the bed, it could bump up and down pivoting at the hinges - especially during its time in the warehouse on the conveyors - and possibly make the spool pin into what looks like your only true casualty. If it was broken in shipping, the other piece should be in the box. There's a good chance there's a corresponding divot in the underside of the top too.
The motor likely just needs its adjustment screw tightened. All in all, the fact that it survived that sort of packing is extremely lucky.