The regulator in the ECU can be "bypassed" with an aftermarket external regulator, common hack/fix on vehicles with the regulator in the ECU.
But I agree with bjm, get the original alternator back and find someone else to refurbish it. Good auto sparkies have a test/refurb bench ready-to-rock.
Once you've got a confirmed output from the alternator (by spinning it up on a test bench first.), confirm/fix the plug wiring and then worry about whether the regulator or exciter circuit have been damaged.
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