12 feet is 3.6 meters.
That is enough for a tight coupling between the motor wires and the switch wires. No doubt about that.
Can you make a drawing, how do you connect 6 wires to a 4 wire stepper motor and still have enough wires for more than one switch?
Are you mixing a ground signal ?
Does that cable have pairs of wires that are closer to each other, like in a twisted pair ? Use the most paired ones for the stepper coils.
You can add capacitors at the limit switches and at the Arduino. For example 10nF. Perhaps even a LC or RC filter.
I would consider a current of 20mA normal in this situation for the switches. That means that your pulldown (or pullup) resistor could be as low as 270 ohm. I think 470 ohm is a good value, could you try that ?
I agree with LarryD: limit switches are normally closed to ground. Can you change it ?
Some filtering in software is always good with switches. Perhaps a filter that averages the switch input during 10ms.