The only way to do the rear crank seal is to remove the box, these engines are pretty bad for leaky crank seals so it'll most likely be that. Can be severe in the way of causing premature wear on a brand new expensive clutch. If you can select all gears at speed id say the box is fine, the syncros normally go first, could try changing the oil and see if it sorts the noise out but i suspect the release bearing is making the noise, any non Toyota OEM bearing is shite.