How to edit stylesheet to change automatic numbering of Reference type to numeric, not alphabetic?

Check out the default style for "Reference":

CurrentValue[{StyleDefinitions,"Reference", CellFrameLabels}]

{{Cell[TextData[{CounterBox["Reference", CounterFunction :> (CharacterRange["A", "Z"][[#1]] &)], "."}], "Reference", CellBaseline -> Baseline, TextAlignment -> Right], Inherited}, {Inherited, Inherited}}

The CounterFunction overrides the default number output and converts it to letters. Just eliminate the CounterFunction to have numbers:

SetOptions[
    EvaluationNotebook[],
    StyleDefinitions -> Notebook[
        {
        Cell[StyleData[StyleDefinitions->FrontEnd`FileName[{"Article"}, "JournalArticle.nb"]]],
        Cell[StyleData["Reference"],
            CellFrameLabels->{
                {
                Cell[TextData[{CounterBox["Reference"],"."}],"Reference",CellBaseline->Baseline,TextAlignment->Right],
                Inherited
                },
                {Inherited,Inherited}
            }
        ]
        },
        StyleDefinitions->"PrivateStylesheetFormatting.nb"
    ]
]