Since there was no rule saying that each one had to be returned to
the original cylinder
(they are, after all, identical) I didn't bother with that. ...And I
keep track of which one goes with
each cylinder. No rule against that, you know

Right. With stock injectors all the same size, there is no requirement
that they go back into the same cylinders, and as far as I know,
nothing that really stops you from deliberately moving them around.
Where the FAA has gotten concerned in the past is where they are
specifically sized (TCM, for example, makes three sizes of injectors
for the same engines). What a lot of people were doing was ordering
some of the "other sizes" and swapping them into the mix, in an attempt
to even out the fuel flow. Or worse (in the FAA's mind), simply using
an abrasive wire to open up the injectors themselves.