Maybe a slightly discharged battery but OK.
Same as above. Resistance in the circuit. Since you've interconnected the battery and alternator feeds, the resistance is either shared (such as battery to stud on relay) or its in both the alternator and battery feeds to the main splice.
Need to be looking voltage drops and checking for whether the voltage follows the rpm.
??? Do you mean after you shut the engine off?
You should get the exact same results with the wire removed. The only difference is the ammeter will show the amount the battery is charging when the engine is running.