It would be great to have a public and debugged set of equations! Donald Hanson wrote up equations for the 6522, which make for a compact representation.
There's a difficulty with equations, just as with simulation, which is the bidirectional pass gates which connect the busses. Cause and effect flow in both directions, depending on the datapath operation.
I think the "Breaks" project's approach, which has produced a coloured map of the logic, is promising. If those patches are indeed relatively isolated, each one could be described independently, and the outputs should have meaningful functions which could be named descriptively.
It's appealing to keep close to the original layout: it will, to some extent, minimise long-distance connections and clump together related gates. Balazs' schematic and Breaks' colouring should both be helpful.
Take a look too at a couple of threads by "Xor" who was tackling the same kind of project:
viewtopic.php?p=13216#p13216viewtopic.php?f=10&t=1747Cheers
Ed