This was always the easiest part of the entire setup 
I just made a fresh install, then I copied over my share partition from my old to my new install. Maybe this was bad?
when I boot I have to use the keyboard to control anything, if I go into controller settings I'm missing the "Configure a controller". I'm not sure how to set it up now?
Yeah, in this case it's wired. I did some more playing with things and found out that unplugging the usb and plugging it back in crashes ES. If I do it slowly, its ok. I'm pretty sure all of this is somehow related to the kernel. Not sure what kernel reto pi uses or recalbox for that matter but I only recalbox does these things. I could maybe grab some dmesg logs on this.
Not sure if this is related but I'd be pretty surprised if not. I just noticed unplugging my HDMI cable kills my usb devices. I bet what is going on here, is just that. The OS is changing screen modes or sleeping and the usb can not Handel it. This is not true on most os's that use the same kernel. IS there a way to have the kernel not shut off usb?
@docbobo has explained my issue well.
No NAS, but seems it[censored] and miss now. Sometimes its ok. Not sure what causes it to loss the password.
After I reboot the passkey for wifi is a long string of some code staring with 3 letters and a ':' (i.e. ecm:......) and no longer connects till I remove that code and put my passkey back in.
I have read many threads on this and recalbox offers no solutions? Since there is no sudo we can use the
sudo sed -i
fix. After some games play for x minutes it comes out of the game and sleeps, rendering some controllers useless. If the unit sleeps you can not exit sleep mode with some controllers as well, so you have to reboot it. All of this could be fixed by disabling sleep. Looks like ES only have a max of 30. IS there anyway to kill all sleep operations?