Congrats on your successful overhaul.
Regarding the hamburger menu, you have the chance to add a label inside the theme settings to fix this issue.
I guess there is no other way to make this warning disappear. Setup a label and hide it with CSS won’t work.
Maybe anyone else got another idea about it, but I guess, this is exactly what the warning is about.
As soon as a warning forces me to change my design, it is always difficult for me to find a right balance.
The Blog/Portfolio HTML markup seems to be built in a way, it is not possible to get around that at the moment, unless you know PHP I guess. Wouldn’t recommend any jQuery/CSS hacks at all, but that’s up to you.
Regarding your 3rd issue, you could replace the link text by something not that generic. E.g. “get more insights”, or whatever you think fits best to your site. That should resolve this instantly.