There is no reason not to cut those front factory frame rails out. They are in the way plain and simple. You are going to have issues getting your pipes to fit because of them. Cutting them out would not have weakened the integrity of the frame at all and they would have allowed for a much cleaner pipe install.
So you installed the swingarm, rear sprocket and ran a chain between it and the motor? If not, I would almost put money on you have chain alignment issues. It doesn't take much to throw a chain.
I am criticizing the work because first and foremost, you posted it on my public forum for the whole world to see. Furthermore, I have built two conversion bikes and I know what it takes to build them.
I think it's funny that you think cutting out the front rails is half assing it and taking the easy way out but rigging up some plate to check motor alignment instead of putting the swingarm on with a sprocket and chain is not.