The guys at http://visual6502.org/ made an amazing simulation of the real 6502, at the hardware transistor level! So finally no more secrets about the 6502!
Working from a single 6502,Â they exposed the silicon die, photographed its surface at high resolution and also photographed its substrate. Â Using these two highly detailed aligned photographs, they created vector polygon models of each of the chip’s physical components – about 20,000 of them in total for the 6502. Â These components form circuits in a few simple ways according to how they contact each other, so by intersecting our polygons,Â they were able to create a complete digital model and transistor-level simulation of the chip.