Just for the sake of lateral thinking, have you considered driving the existing analog pots mechanically? That ought to be very simple using ordinary hobby servos with a belt or flexible coupling to the potentiometer shaft.
If you're pursuing the electronic approach, I'd look to see whether any of these pots are just being used as voltage dividers between supply and ground rails to generate a variable DC voltage. If so, you have the option using using a DAC instead of a digital pot.
The dual pot sounds as if it may be a redundant input used to detect failures on a critical input, with the two tracks wired up in reverse so that they produce opposite signals so that no single hardware failure can cause a spurious input. In that case you could replace it with a pair of simple pots (or DAC outputs) and just control them together to produce the right combination of signals.