I think we all come to the table with different ideas, so I would advise doing what you want. I wanted my Nobler to be close to stock as possible, so I used most of the hardware provided--but did change the leadouts. I was/am a little worried about those clevises, but used them nevertheless. One "nice" thing is that I can easily inspect the things since I can remove the wing, and also make a simple cut in the monocote near the tail to get access to the elevator clevis.
Now whether it will fail catastrophically, I am not sure.
About the motor mounts, it might depend upon the engine you use. My Brodak40 feels pretty smooth, so I am not really worried. If you plug on a Fox or other potential shaker, maybe that might be a worry.
My attitude was to get it up and going as soon as possible--I needed a flapped stunter, so rather than working up anxiety attacks about everything, I just went with the flow. So far, so good. At least I am able to perform a full pattern now (well it looks like one to me anyway!). If something lets go, I'll report it.