How about implementing your CPU on a FPGA? It should be easier to verify the physical hardware hasn't been tampered with.

e.x. https://en.wikipedia.org/wiki/Amber_(processor_core)

Of course it would be orders of magnitude slower than a modern CPU.

"To add to this madness, even if you design your own chips and software stack, you the fab that printed your chips might have modified your design" True, changes can be so subtle, remember how the Playstation were hacked on the basis of altering the current provided to the CPU?

"His approach is clever and is known as a “glitching attack“. This kind of hardware attack involves sending a carefully-timed voltage pulse in order to cause the hardware to misbehave in some useful way" from http://rdist.root.org/2010/01/27/how-the-ps3-hypervisor-was-...

edit: typos