UncleFester wrote
I still wonder if the slow speed wire should be permanently disconnected from the original fan controller though.
If I understand his
wiring diagram correctly, the slow speed wire from the VAG fan controller is used to switch the Nime box on. I'd expect his instructions say to cut that wire, connect the controller end to the Nime box "on" input and clip the other end out of the way, wrapping the end up to insulate it. (It leads to the failed resistor, but there's always the possiblity that the failure has only gone high-resistance rather than open-circuit.)
So you can't disconnect the slow-speed wire, it's telling your Nime box when to start working (in slow-speed mode).
I can see a couple of changes that might
help.
One is to turn the power supply wiring to the fans into twisted-pair, by getting some wire of a similar diameter and twisting it together with the power wire, all the way up to the VAG fan controller, and doing the same down to the output wire from the Nime box. Twisted-pair wiring drastically reduces radiated noise. You'd have to earth one end, but ONLY one end - probably easiest to do at the Nime box, making sure the thicker wire paired with the power wire is connected too. It's no good wrapping the earth wire round the power wire though - they have to be twisted together, like a rope: the geometry matters.
Another is to switch the Nime box by XOR-ing the low and high speed fan signals, so that the Nime box would switch off once the high speed relay in the VAG fan controller closes. I may be worrying too much, after all the FET in his box will have 12V on either side of it once the high-speed relay closes, but the 555 timer circuit will still be running and there may be just enough leakage to upset something.