Right before you battle Lugia, is that where I can save and then soft reset to try to get a shiny Lugia? Or do I have to save before it even appears?
Yes,all Pokemon can be shiny bt you have to be lucky!There is 1 chance in 8,192 that you will meet a shiny ,so keep trying!
edit:Im pretty sure that both choices are fine but better save before it even appears.