As far as I understand, the fundamental problem between the pi and new CEM40s is that the mount uses a USB hub chip that does not have a driver in the linux distribution. Beyond that, there seem to be a variety of things that can cause the connection to act up.

My eventual solution involved 4 separate actions:
1) Put a powered usb2 hub in between the pi and the mount
Some sort of intermediate usb hub is going to be necessary until the linux distro catches up, if it ever does. I am not certain the powered hub is required for me because I added it before taking step #3
2) Used a 3rd-party usb cable to the mount
Not 100% sure this is necessary, but my mount is rock-solid reliable now and I'm not changing back
3) Swapped 12v power supply.
Not the one the mount uses, I still use the one from iOptron. I use a 2nd 12v supply for the camera cooler, dew heaters, etc. I was testing indoors with just the mount powered and all was well. Then I plugged in the 2nd 12v supply immediately (and frequently) the mount dropped the usb connection to INDI. I tried a different 12v supply and all is well. I assume the supply I started with generates a lot of RFI
4) Wrapped a velcro around the usb plug and the 12v plug at the back of the mount

I know #4 sounds weird. Myself and some others noticed that the usb connection at the mount is not completely snug (and for me it is much worse with any usb cable other than the one supplied by iOptron). I think I was getting some sporadic physical disconnection. It would disconnect during a meridian flip, for example. Seems to only be a major issue when very cold, but, again, it's working so the velcro stays. The purpose of the velcro is to apply a (gentle) sideways pressure to the usb connector

Without the hub, the pi simply never connects to the hub in the mount or any of the mount's devices (FTDI, iPolar). After adding the hub it was connecting, but suffering from frequent 'Read error' messages from the mount. Since taking all 4 steps I cannot recall any Read errors. The mount always connects and stays connected.

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