It seems logical. However http://ecmweb.com/qampa/code-qa-identification-circuit-conductors saysA yellow wire tagged with green tape on both ends to indicate ground has been accepted by our local building inspectors.
Equipment grounding conductors can be bare, covered, or insulated. Insulated equipment grounding conductors size 6 AWG and smaller must have a continuous outer finish either green or green with one or more yellow stripes [210.5(B), 250.119].
On equipment grounding conductors 4 AWG and larger, insulation can be permanently re-identified with green marking at the time of installation at every point where the conductor is accessible [250.119(A)].
That is a tough read.I think you should review the NEC code
My well people did not use the yellow wire when reinstalling my 2-wire pump, but they did splice the existing red, black and yellow underground feed wires up to the well cap, in case I needed it in the future. I am happy with what they did, and I would be happy with what you do.
I don't know what the grandfather rules would require, but your interpretation makes logical points. Certainly if your inspectors require what you do, that is what you should do. But here they don't look for that.