According to Bulbapedia, and my own experience, the story should progress as such:
After going to Mahogany Town, go to Lake of Rage and either Catch or KO the Red Gyrados. Then go fight Team Rocket in the tiny shop in Mahogany Town. Then fight the Gym in Mahogany Town. Then go to Goldenrod City to fight Team Rocket in the Radio Tower, and get the Silver WingSS/Rainbow WingHG from saving the Director.
The Silver Wing/Rainbow Wing allows you to get past the Rage Candy Bar Salesman, not curing Ampharos (you only need to do that to challenge the Olivine Gym). :P
Hope I Helped!