Why do you "have to" clear all of these? Some of this is completely unnecessary or is a sign of other issues.

1. This I can see - it has valid uses. Set the jumper to CLR, then boot up the system - you will see a message that the NVRAM jumper is installed. At this point, you can power off, unplug, and put the jumper back in its original location.

2. Yes, there might be very rare situations where you might need to do this, but only if the system has no OS and the cache is not cleared on subsequent reboots, and even then it is more likely because of bad RAID memory or battery than cache needing flushed. On newer controllers, you can do this from the controller BIOS.

3. This is cleared on every reboot - there is NO valid reason for data to be kept "alive" in the video RAM. If you are super concerned, power down, remove power,  hold power button down for 10 seconds.