Honest post here - I have had 2 pairs of Vaporfly 4% and at least 7 Zoom Fly pairs.
ZoomFly
*No problems whatsoever. No pain. Good daily training shoe. A little on the stiffer side.
VaporFly 4%
*First pair I raced in I had no pain but didn't wear the shoe again until my final 4 weeks of my next Marathon cycle. It was only then that after that first race the shoe started giving my little aches on the inside of my knee during my Long tempo runs (22 miles). It eventually went away so my guess is one of my muscles in my leg was probably tight and just needed to stretch. But this didn't start to happen until I used them for my longer Tempos. I did get over 400 miles on them though.
*2nd pair. I raced in these during the 2018 Boston Blizzard. Couldn't feel my feet to begin with from start to finish. Funny thing is the next day my right foot was in pain. Don't know if i was landing properly due to the fact I had no feeling in my feet and legs nor body. Was just too cold and somehow sprung a niggly. I could run on it but It took 4 weeks to go away.
Honest opinion - I'm not racing in them anymore. I have a fall thon coming up and will be using another shoe. Can't take no chances.
Or I just race in the regular ZoomFly. I have no issue with them. I trained properly. One stupid shoe is not going to make a difference. I trust my training.