F4 won’t work unless you edit the cmdline.txt to revert it back to original settings (see my ‘notes on build’ post further up). Otherwise you will have to use SSH instead (that’s what I do).
Roms folder permissions should be fine? I set them all as read/write for user ‘Pi’ (and others). If it’s a problem then SSH in and type:
sudo chmod 777 "/home/pi/RetroPie/roms/"
And that should fix it for you.
As for keyboard navigation – what is confusing you, and is it in ES or or RetroArch?