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are you using a 12’ beam? If not, your beam is a bit high and your chain may not be long enough. What is the distance between your spoil board and the motor shaft plane? (see here)
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The Due has 2 ports on it. One is the program port and one is the connection port. Only one of them will work, but the firmware version you are using with determine which is the correct one. One issue with removing the controller from the case is that the due controller shield has fewer pins, so they tend to separate if not held together firmly with the case. Some shields have separated slightly and that causes weird behavior as the shield with the movement chips don’t communicate correctly.
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When the initial M2 came out, there were a few users I tried to help who ended up with bad Due boards. Makermade covered them as far as I know and that fixed it. I don’t know that the root cause of the controller problem was ever shared, but the tell-tale sign of trouble was the communication terminal would show random garbage characters and sometimes makerverse would not “detect” the controller attached. There has been speculation that the eeprom was corrupted somehow. You might try wiping the controller, clearing the eeprom with the erase command has helped at times and at other times, replacing the Due has helped. The erase command is on this forum somewhere. You’ll have to search. It is a terminal command you type in makerverse (starts with $) and it resets all the memory. You could also delete your .makerverse file (which will erase the “machine” in makerverse and you would need to start over. Either one of these will require reconfigure and recalibration.
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20’ usb without an active amplifier is likely to be a problem, but may not be the issue. The not-so-quick fix is the 1’ cable and a raspberry pi. The 10’ cable should be better, but a 6’ would be certifiable. Certified USB cables are 6’ or less. The USB logo is only allowed to be used with components that have been tested and certified by the USB working group. If in doubt, look for that trademarked logo, not just the text specifying USB for cables and devices that are mission critical.
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I installed a light switch on my maslow that switches an outlet that is connected to the shield power. This allows a quick switch toggle to stop the sled movement, but not kill the software, so it can be recovered. Webcontrol actually stops the movement and cancels the rest, but Makerverse will try to continue the move when you turn the sled movement motors back on. Something to be aware of.
I hope some of this is helpful.