If its that bad I think you need to take some place . Like dealer or a independent and have them dowload codes and look bike over . We can't fix over internet and I think this needs real trained help.
You have 2 major problems clutch (why air in line) and fuel mileage . Did the big drop come when you changed pipes? Is the o2 sensor hooked up, . I would get all this fixed then I would worry about a fuel controler and air box mods . 1 step at a time solve present problems now Then worry about add ons.