You can add an entry to your sudoers file so that the setpci command can be run without prompting for a password.
First run the following commands to open the sudoers file for editing...
Now add the following line to the bottom of the file replacing username with your actual username.
Hit CTRL+x and save the file and then exit your root shell.
username ALL=(ALL) NOPASSWD: /usr/bin/setpci
You should now be able to run 'sudo setpci -s 00:02.0 F4.B=15' without being prompted for a password, so just add the command to your startup applications using the 'Startup Applications' application.