Kernel panic when try to boot from a USB with El Capitan

Why are you reinstalling macOS? The issue with the installer may be the same issue which caused you to reinstall macOS. Not sure about the "TLB invalidation IPI timeout" part, but the "CPU(s) failed to respond to interrupts, unresponsive CPU" indicates to me you may have a hardware issue assuming you created the macOS 10.11 USB installer correctly.

Create a bootable installer for macOS - Apple Support

Try using a different USB stick or drive. Try using a different USB or Firewire port.

Disconnect all other external devices in case one of them is causing a problem.

And what do you mean by "that got some hardware modified"?

I believe it is a hardware issue.

To test my theory that the difference between macOS 10.6 working and 10.11 not working is related to the 64 bit Kernel and OS, try booting Snow Leopard into 64 bit mode. Immediately after the startup chime, press & hold the 6 + 4 keys (should be able to release once the Apple logo appears). You need to use a wired keyboard to access the special startup modes. Once booted into macOS, Option-click the Apple menu and select the first item to access the Apple System Profiler. Click on "Software" in the left pane and check the right pane to see whether the item "64-bit Kernel and Extensions" show "yes".

Only clues there, Apple has made Logs pretty useless...

IOAudioFamily

BSD process name corresponding to current thread: kernel_task

Boot args: container-dmg=file:///Install%20OS%20X%20El%20Capitan.app/Contents/SharedSupport/InstallESD.dmg root-dmg=file:///BaseSystem.dmg

So, have you disconnected any & all 3rd party gadgets?

macOS has changed how it works over the years...and there are five years between them, perhaps 10.11 is accessing the hardware in a slightly different way. I believe 10.6 only ran as a 32 bit OS, unless the user manually told the OS to boot as 64 bit (10.6 had both versions). macOS 10.11 is booting as 64 bit. So the CPU is being used differently.

Since this is a Mac Pro tower, I have seen some posts from more a more knowledgeable contributor which has mentioned that the heatsink, I believe for the Northbridge or Southbridge chipset on the Logic Board becomes loose (broken) over the years. Not sure if it pertains to this exact model, or just one of the later models. I don't recall the symptom...would have to check out the threads in the Mac Pro forum.

I suspect it is the 32 bit OS is "working", but the 64 bit OS is failing due to a hardware issue with the Mac Pro.

Have you tried disconnecting the power lead to the Optical drive at least?

Let's disconnect the power lead & the Data cable from the Optical Drive & see if that helps.

fdamore1984 wrote:

i can try to download El Capitan directly on Snow Leopard and start installation instead of using USB, but probably he will go on bootloop

That is a good test. As I mentioned before, the quality of USB sticks is extremely poor and Macs are very picky about the drives used especially for booting.

I guess there must be something else with El Capitan that differs from Snow Leopard.

I still think there is a hardware issue with the Logic Board. I know the Mac Pro forums have multiple posts which a much more knowledgeable contributor has written which mentions a heatink or something similar detaching or loosening up. It may be hard to detect. You may need to look back a year or two to find the relevant posts.

Looking more & more like a hardware issue... CPU:s).

TLB invalidation IPI timeout - Apple Community

Log isn't showing here.

I believe you nailed it.