Use these commands to get rid of the controller config file:
cd .emulationstation
sudo rm es_input.cfg
In case you can’t see the screen (I’ve had this problem, too), I believe the order of keys it runs through is:
up
down
left
right
select (choosing a rom)
back
menu
page up
page down
I’m not sure how to fix the screen resolution, but here are some things to try to see if they help:
1) Switch between HDMI and RCA outputs
2) enable/disable “Variable HDMI resolution” in the retropie_setup.sh menu.
3) Try it on a different TV/Monitor.