Good point! Still have to work on the flow tracking a bit, but here's the visualization tool already,

https://github.com/laanwj/xray6502

Bravo! That's certainly a step forward for visualisation.
Yes, I ended up writing a new tool '6502 X-Ray' to explore, I wanted something to quickly see the connectivity.

I'm baffled by the complexity of even such a small chip. And as it was back in the day it's all drawn by people, it's even more ...

Data flow tracking in various forms is quite common for software these days. Seeing the awesome visual6502 data I wondered "is it possible to do data flow tracking on a transistor level, and get sensible output on a per-instruction level?".

I started out with perfect6502 simulator and added tag ...

Good spot - something isn't right there. If you toggle the layer visibilities you'll see, I think, that this node corresponds to a protection structure - which would made sense if clk1out was an input.

And in fact, in the case of the 6501, this pin is an input! We believe the 6501 and 6502 differ ...

I think I found a small erratum in the visual 6502 data, though I doubt I'm the first to spot this:

t2730 pulls node 860 to ground, but node 860 is not connected to anything.
From the context I suppose it should have been connected to node 1163 clk1out.

See http://www.visual6502.org/JSSim/expert ...