I am happy to hear your second attempt went much smoother.
If USB communications are interrupted, the software should let you know in two separate locations as indicated below. You won't be able to click any buttons (print, calibrate, bake) if the printer is disconnected. Looks like you've encountered a bug, I'll make a note of it.
As you advance through the software, the printer will automatically prepare the corresponding tool as soon as you enter relevant step. For example, as soon as you enter the Probe step the printer will start moving
The tool preparation sequence will:
1. Raise the carriage first to ensure nozzles don't get damaged.
2. Home the carriage in the X & Y axis
3. Ensure the right tool is mounted (i.e - A dispenser is not mounted when it expected a probe)
4. Lower the tool to the bottom circular shaft (bottom Z switch). This sets our 0 height.
5. Perform XY alignment by descending into the larger hole and contacting the 4 limit switches
6. Raise the carriage and return to (0,0).
Whenever the motors are released, the tool preparation sequence needs to be executed again. In a typical print, it will only happen twice, once for the probe and once for the dispenser.
During tool preparation, the buttons will display 'Please Wait', once the sequence is complete the buttons will behave as normal.
Please keep your feedback coming. We love hearing about your experience.