Possibly offtopic, but a neat project with interesting analogy to mind uploading:
Some people managed to scan, using a microscope, a MOS 6502 microprocessor (Apple II, C64, NES), and simulate it at the level of single transistors. This neatly circumvented all the problems with inaccurate emulation, unknown opcodes etc., and even allowed them to run actual Atari 2600 games without having to know anything about 6502's inner workings.
Presentation slides about the project are here.
Note how late it happened, and how useless the results are, though. Practically nobody uses IT systems that are scanned and emulated versions of the previous generation of technology.
Yes, late, and yes, slow. But it's what you have to do when you don't understand the thing you wish to duplicate. Making a brain is one thing, making a specific brain is another.