Figured it out.
You will need a program called "putty" to SSH into Batocera. Follow these steps:
Open the Main Menu in Batocera (start button on controller), go to network settings and make note of the IP address.
Open putty on the computer you installed it on. Type in the IP address on Batocera under "host name" in putty and press enter.
You will now see a black screen that reads "login as". Type "root", then enter. Then type "linux" as the password.
Now enter this next command exactly as typed:
mount -o remount,rw /
Then press enter. If entered correctly it should look like it did nothing. If prompts or information populate you did not type it correctly. Please make note of all spaces between the characters.
- Enter this next command exactly as typed:
cp /etc/X11/xinit/xinitrc ~/.xinitrc
Then press enter. If entered correctly it should again look like nothing happened.
Plug a keyboard/mouse into your Batocera machine and press F1 to enter the file system.
Click on the "system" folder. Then click "view" from the top menu and then click "show hidden". You should now see a file named ".xinitrc"
Double click to open the file and scroll down about half way until you see this:
"# rotate the screen"
"# xrandr -o left"
"# xrandr -o right"
"# xrandr -o inverted"
You will need to remove the hash before the option you want. Example for left rotation:
"# rotate the screen"
"xrandr -o left"
"# xrandr -o right"
"# xrandr -o inverted"
Once you made the change click "save" from the file menu. Then "quit" from the file menu. Finally click "close window" from the file menu. You should now be back at the Batocera home screen.
Open the Main Menu in Batocera again. Then go to "quit" and choose "restart system".
Enjoy your new vertical orientation Batocera!
If the screen is rotated the wrong way go back into you ".xinitrc" and try a different rotation option. I hope this helps anybody else having this same issue.