I think your bed is rocking back and forth, so that on the left-hand scans the height has one value, and on the right-hand scans the height has another. This could be because the x belt is pulling off-center on the carriage, or the carriage is just loose.

@gtj0 I'm printing the Prusa rc3 face shield frame, and sending them off to https://www.wethebuilders.com/projects/11 who are assembling them and distributing them at cost to the Maryland area. I will pass 50 printed by Monday, and I think many thousand have been produced by the whole team.

I would always add an explicit line, so you are not dependent on defaults, and so that you can easily see what to change if there is an issue. 'hidden' configuration can be very hard to diagnose.

As mentioned above, a PT100 sensor is very sensitive to wiring resistance. To really get accuracy out of them, they are generally used with 4-wire connections. A 2 degree error on a PT100 is less than an ohm, which would be easy to find in wiring. Is the daughter board capable of 3-wire or 4-wire connections? If so, the PT100 would become your thermometer of reference, as it is very good over a very wide range.

I put a PT1000 on my DuetWiFi for the hot end. I now trust my high-temperature readbacks to a degree or two. That is limited by the accuracy of the bias resistor in the readback bridge. With a PT1000, of course, wiring resistance is much less significant.

@William That is true with slic3r, at least on the Mac, but PrusaSlicer has fixed that issue. I can upload from PrusaSlicer without keeping an open connection in a browser.

The probe not being pushed all the way on the touch means you may have set your probe offset wrong. The printer will give up probing if it has to go below the programmed low limit on z. If you are zeroed just about where the probe would switch, it might give up too early.

Is it possible the sensor itself is loose? The wiring could be intermittent, but usually that results in reading extremely low temperatures, and much more erratic behavior. If the thermistor is in intermittent thermal contact, it could cause small jumps like this.

Steppers, even cheap ones, can generally be operated at a surface temperature of 60C with no worries at all, and probably 80C if you want to push them hard (maybe with a shortened lifetime, but not immediate failure). If you can put your hand on them more than 5 seconds, they are fine! You are running yours very gently.
For the past month, I have been pushing mine to 60C surface temperature to run the printer faster to print frames for face shields. I normally stay around 40-50C.

The Duet3D is putting the motor to sleep, reducing its current to the fraction specified in the idle current setting. This fraction may be too low for your machine.

I would always add an explicit line, so you are not dependent on defaults, and so that you can easily see what to change if there is an issue. 'hidden' configuration can be very hard to diagnose.

You should be able to enter these commands from DWC while the printer is running, as long as you are careful not to type the wrong command. And then you should be able to plug in the sensor. This stuff should have no effect on a running print. Make sure you discharge static before you plug in the sensor, though.

I can vouch for Filastruder. Quick shipment, and they aren't out of things. I happen to be close enough to them that everything arrives in 2 days (they are near Atlanta, I am near Washington, DC). Quality seems excellent. I've been buying the Masterspool filament (comes without a spool, then you buy a couple reusable spools they sell). Loading the spools is quite easy. They aren't the rock bottom price, but the $25/kg (shipping included if you buy over $100) isn't crazy, especially for US made filament.

I'll bet the new stepper is an 0.9 degree (400 steps/turn) instead of the more common 1.8 degree (200 steps/turn) motor.