There is not mathematical way that Im aware of for compensating for a torque converter. It would be complete guessing. Its the same as a slipping clutch how do you guess how much power is being lost there.
Wind resistance is taken into account and added as drag hp. You can check the frontal area and drag coefficient for your vehicle by looking in File -> Car Editor.
Virtual Dyno has been proven to be very accurate on 14 other forums.
Also you arent deforming your tire that much. Not enough to make a difference. These differences are from data in the logs. The issue with tires that you mention is a valid point in dragsters but not in your car.
