If you can monitor them, check the signals going to the clutch and the ECV. If those look normal, then you may have a bad clutch.
As for the auto feature problem, I just can't tell.
I'll take another look at the FSM later and maybe I'll have a eureka moment.
Since no body else seems to have any suggestions and I don't have a real good grasp on how the HVAC is controlled, you may be better off taking it to a dealer and letting them troubleshoot with CONSULT.