Yes, the plates should sit flat next to each other and not overlap each other on the rag joint sprocket assembly as shown in your picture, so that indicates some problem there. How many spokes does your wheel have on each side? I really suspect your rear sprocket/rag joint assembly is the root of all your problems (pushing you to change the motor mount, which is another problem)
Is that one bolt rear mount made of plastic? Either way, it doesn't seem secure enough IMHO, you need to use the two stud mount that is supplied with the kit if you ask me. I don't see a picture of how this single bolt mount mates with the motor, but it looks like it would make things be a bit cockeyed, and will not stand up to the torsion forces that will be on that motor mount. (as you learned the hard way)
One important picture you didn't post, and what you should be looking at to see what you need to do to make the chain alignment proper, a view of the chain running from the motor back to the rear sprocket. If when the motor is centered and mounted with all 4 studs your chain rubs the mount, then you need to adjust the rear sprocket somehow. If that means you need to buy a sprocket that is dished to one side so it puts the chain further from center, or putting a thicker rubber behind the sprocket on the rag joint... or maybe your tire wasn't mounted straight originally and caused the whole problem?