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I second the use of Eppy, which is in Python.
I would also recommend OpenStudio, if you want to start using that ecosystem. This kind of workflow is precisely what Measures (which are in Ruby) helps accomplish. You would basically have a Measure for 2. and 3. where the Measure changes the baseline model to have HVAC 1 or HVAC 2. Thus if you change the baseline model, the measure should work exactly the same (if written well).
I think without some form of scripting, this is an exercise in patience and attention to details. I would highly recommend looking into a scripting option.