Copy files from the "retropie setup files" folder to the appropriate folders on the Pi via FTP.

Edit /opt/retropie/configs/all/videomodes.cfg and add this. This should be the only text in the file:

lr-catsfc_render="config"
lr-armsnes_render="config"
lr-picodrive_render="config"
lr-fba_render="config"
lr-fceumm_render="config"
lr-gambatte_render="config"
lr-pocketsnes_render="config"
lr-snes9x-next_render="config"
lr-handy_render="config"
lr-genesis-plus-gx_render="config"
lr-gpsp_render="config"
lr-pcsx-rearmed_render="config"
lr-nestopia_render="config"
lr-mednafen-pce_render="config"
lr-mednafen-pce-fast_render="config"
lr-tyrquake_render="config"
lr-prboom_render="config"
lr-vba-next_render="640x480"



Edit /opt/retropie/configs/<emulator>/retroarch.cfg files and add these lines TO THE BEGINNING of each

Neo Geo Pocket Color / Neo Geo Pocket

video_fullscreen_x = 1920
video_fullscreen_y = 1080
custom_viewport_width = 480
custom_viewport_height = 456
custom_viewport_x = 180
custom_viewport_y = 12
aspect_ratio_index = 22
input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.500000
input_overlay_scale = "2.000000"
video_smooth = false


Gameboy / Gameboy Color

video_fullscreen_x = 1920
video_fullscreen_y = 1080
custom_viewport_width = 1180
custom_viewport_height = 1044
custom_viewport_x = 370
custom_viewport_y = 12
aspect_ratio_index = 22
input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.500000
input_overlay_scale = "1.000000"
video_smooth = false


Gameboy Advance

input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.500000
input_overlay_scale = "2.000000"
video_smooth = false


Genesis / Megadrive / SNES / 32X

video_fullscreen_x = 1920
video_fullscreen_y = 1080
custom_viewport_width = 1194
custom_viewport_height = 896
custom_viewport_x = 363
custom_viewport_y = 91
aspect_ratio_index = 22
input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.500000
input_overlay_scale = "1.000000"
video_smooth = false


NES / FDS (Famicom Disk System) / PCE

video_fullscreen_x = 1920
video_fullscreen_y = 1080
custom_viewport_width = 1280
custom_viewport_height = 960
custom_viewport_x = 319
custom_viewport_y = 59
aspect_ratio_index = 22
input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.500000
input_overlay_scale = "1.500000"
video_smooth = false


PC Engine / Turbo Grafx 16

video_fullscreen_x = 1920
video_fullscreen_y = 1080
custom_viewport_width = 1236
custom_viewport_height = 928
custom_viewport_x = 341
custom_viewport_y = 75
aspect_ratio_index = 22
input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.500000
input_overlay_scale = "1.000000"
video_smooth = true

FBA

video_fullscreen_x = 1920
video_fullscreen_y = 1080
input_overlay = /opt/retropie/emulators/retroarch/overlays/1080p_4-3/Scanlines_4x_1080p_Borderless.cfg
input_overlay_enable = true
input_overlay_opacity = 0.7500000
input_overlay_scale = "1.000000"
video_smooth = false