Last night in the darkness of my garage I only quickly looked into the holes where the two bolts labeled #2 in your diagram should go. I thought I saw some bolts, but when I looked in daylight today I don't see any bolts. I'm wondering if I'm reading the diagram correctly.
In the first photo below you see the two openings in the blue frame area (above the motor) in the lower left and upper right. The chainstay has been detached and moved a bit to see the holes better.
The second photo shows a closeup of the lower left hole and the third photo shows the upper right hole.
In the lower left hole I don't see any bolt, just threads. Did the bolt fall out some how?
In the upper right hole it looks like the head of the bolt may have broken off, but I'm not sure. There was a loose washer in that hole which is removed in the photo.
Also, in the third photo there are two holes in the motor. Compared to the upper right hole in the blue frame, these holes are in the black area and one is directly below and one is to the left and a bit below the upper right blue hole. I see threads in those two motor holes. Are they missing bolts too?
This is very strange since I didn't even know those two bolts existed before and thus never tried adjusting them. I guess one bolt could loosen and fall out over time, but I don't see how a bolt head could break off.
I do have about 1000 miles on the bike, most all from riding in spring and summer of this year.
Does your shop manual give the part numbers of the apparently missing/broken bolts, lock nuts, and washers? Unless I'm missing something, I guess I have to order some parts from a Yamaha ebike shop. Also, the four bolts holding the chainstay seemed to be torqued to about 15 Nm before I removed them. Does your shop manual show if that is the correct torque for those four bolts (for when I put it back together)?