Is it possible to configure a system (included changes to programs) so that nothing can interfere with a few RT threads? I have an audio and video thread in a program, and they are running as SCHED_FIFO, but so many things can interfere with those two threads, such as USB plugs/unplugs, cron log rotations, disk access (PIO flash disk), ssh logins, etc. I really would like to shore up performance here. I am not using Ingo's RT patches, but I still see people talking about turning off things like cron and server processes to prevent xruns when using Ingo's RT patches. While I have turned off cron, turning off sshd and the web server aren't options. I want to instead somehow make sure that neither can every interfere with the AV threads, even if it means that SSH and web traffic are extremely slow.

You must use the rtirq package. It is a boot script that use chrt to fix the priorities for different IRQ. The trick is to setup the highest priority to the rtc (the system will hang otherwise), followed by the sound, followed by the other pieces of hardware.