For the riding you describe, don't mess with anything. Take a stock XR400, pop on a baja designs skid plate and just ride it. Don't need to mess with the airbox, jetting, suspension, etc. If you get into competitive stuff like enduros then maybe some suspension work if you are heavier than 160. The stock tank will get you 60 miles of snotty riding. The light is there, it is pretty poor, Baja designs has some solutions to this other than those huge lights. The stock muffler is good.
The XR is ready to ride. If you require a more bike, get a WR.
I'll see you on the trail.