Hi again,
I've been making the migration and tweaks – have come up with a few questions.
To see my site please use URL: http://eranco.com/?passkey=word

1. On my home page the first images to load show very small thumbnails in the masonry. The ones that load on scroll are all fine. I've checked backend and all my featured images are big enough for retina and when I compare posts that look correct vs. posts that have small images on homepage, I can't seen a difference. See here: http://imgur.com/a/YF7te

2. Logo. In Chrome it's huge. In Safari its tiny. See here: http://imgur.com/a/YF7te
We can see it resizing too and it also lags on scroll and sometimes appears twice on scroll.

3. Footer widgets have disappeared. We have 4 selected in option, rebuilt them all. And had them working fine. And now suddenly all widget in footer are gone. No new plugins added so its unlikely to be a compatibility issue. Hide footer widgets is off.

4. Regarding Question #1. We just changed number of posts to "unlimited" and now ALL our home page images are tiny. Weird.