If you find it pretentious, he could go by Jack...the least pretentious name I know!
I love it. How wonderful that you like the name and its a family tradition. I agree with the idea of having a nickname to avoid to much confusion.
We actually have a family name in my family as well, there was been 5 William Georges that I have known of so I think it's a very sweet idea naming your son after his father, grandfather and great grandfather and I don't think Simon John IV sounds prentious at all. Although maybe giving him his own nickname would help stop confusion and the nicknames that have been suggest such as Monty, Si and Johnny are awesome.