Alternator Wiring Question

I'd like to switch to a chrysler alternator, but not sure where I would wire the FLD1 and FLD2 connectors to.

If the Mallory is anything like the MSD, it doesn't care if there is or isn't a ballast resistor. You could install if you wanted. it will run the same.
The Hyfire gets its working power from the connection to the battery positive. It builds a charge and sends through the coil.
Now that connection might be best to leave on or near the battery if the Hyfire is sensitive to electrical noise. It probably doesn't care but I don't know that.

Now to field connections. Take a look at "How to Identify Chysler Alternators".
If you are using a grounded field regulator (as would have been in '65) then connect power from the run circuit to the regulator. Then there is one field wire to the field terminal on the alternator. The second field terminal is grounded to the housing. Simple.

If you are using a regulator for alternators with two insulated field terminals, one terminal of the regulator gets connected to the ignition run wire, and one field terminal gets connected to the ignition run. The other field terminal gets connected to the voltage regulator.