It's closer to your engine than it is the silencer, probably about in line with where you sit, maybe slightly further forward. My gear changes are alright, you could well have a problem with your gearbox, I'm
Not sure to be honest. A way to tell if it's a rattle on the exhaust may be to accelerate in one gear through the revs, then let the engine rev back down while after you stop accelerating. Mine makes the biggest rattle if I do that. Sorry I'm not much help!