Assuming no Nikasil issues & that it's getting colder in your area,
The intake gasket(s) are probably leaking on your engine.
They leak less when warm because they swell up a little.
One source of possible rattling besides engine related: Does it only do it when the engine is idling rough/stumbling? Manual transmissions can make noises like that at very low RPMs. Try pushing the clutch in when it is making the rattling noise. Just throwin' the idea out there.