We've gotten a few reports and have been able to duplicate the extruder wheel "clicking" and stopping intermittently while printing. This is only present when using the adapter and we verified the tool-heads function normally on a Mini 2. We also checked the wiring of the adapter.
I investigated the issue a little and found a solution. Looking through the configuration files I could see the tool-heads with the adapters were set to a much higher extruder motor current than the other tool-heads.
Using the command 'M907 E960' to set the motor current to the same value as the standard Aerostruder before starting a print fixed the audible clicking and the print quality issues.