Changing Y-axis is fairly easy
Names Default To Here(1);
dt = Open("$SAMPLE_DATA/Semiconductor Capability.jmp");
fg = dt << Fit Group(
Oneway(Y(:NPN1), X(:lot_id)),
Oneway(Y(:PNP1), X(:lot_id)),
Oneway(Y(:PNP2), X(:lot_id)),
Oneway(Y(:NPN2), X(:lot_id)),
Oneway(Y(:PNP3), X(:lot_id)),
<<{Arrange in Rows(1)}
);
axis_box_refs = (Report(fg) << XPath("//OutlineBox[starts-with(text(), 'Oneway Analysis of')]//AxisBox"));
axis_box_refs[1::N Items(axis_box_refs)::2] << Scale("Log");
updating colors of reference lines is most likely a bit more difficult and and will depend on where you are getting the limits from.
-Jarmo