You are correct about programming the engines. They both come from the factory thinking they are SB engines. I do not know the tool needed to do so, but I would imagine it is a laptop with the Mercury Software. I don't know if the Rinda tool can make this adjustment. You will need a Mercury Mechanic to confirm what needs to be done.
As for the mechanical indicators; leave them installed if at all possible. They will be more reliable and perhaps more accurate than the electronic ones that come with the drives.