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I just saw a very detailed write up from LT1*C4 and his water pump did not have that hole. The other looks to be for the coolant sensor. I figured I plugged that hole for a reason but it's been many years ago. I was asking because I bead blasted it and noticed a small crack. You can see it on the left hand side. Most likely this did not come off a vette.
That I believe would be for the heater outlet/inlet port. You will need one I'd think. A '92 didn't have that port I believe but '93+ did. Yours being a '91 and a transplant I don't know what you could expect for heater plumbing issues.
The other is for the ETC sensor for ECM as you suspected.
The heater inlet/outlet port changed for various LT1 applications in various body styles. They were all in the same location but varied widely in shape.
The casting "bulge" on the left side of your image is for another coolant port for other applications. That pump varied widely in usage from the 4.3 LT engine (L99 I think) in B-body cars to those in the f-body and then of course marine applications.