Actually, really, truly fixed the permissions issue with the boot file.

calcsetup.sh

@@ -75,7 +75,14 @@ echo "" >> tmpboot.txt
 echo "# set up the size to 800x480" >> tmpboot.txt
 echo "hdmi_timings=800 0 40 48 88 480 0 13 3 32 0 0 0 60 0 32000000 6" >> tmpboot.txt
 
-sudo cat tmpboot.txt >> /boot/config.txt
+touch oldboot.txt
+
+cat /boot/config.txt >> oldboot.txt
+cat oldboot.txt >> newboot.txt
+cat tempboot.txt >> newboot.txt
+sudo cp newboot.txt /boot/config.txt
+
+sleep 2
 
 # Install X server, DM, WM, vim (for some reason), and python stuff
 sudo apt install vim xorg lightdm ratpoison idle3 python3-matplotlib -y
@@ -96,7 +103,7 @@ touch .alreadyrun
 echo "This script can only be run once." >> .alreadyrun
 
 echo "Shutting down. Connect LCD, then power back on."
-sleep 2
+sleep 5
 
 sudo shutdown -h now
 EOF