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Don't get too too worried about metal parts in the oil in a manual gearbox - even in a differential where there is no changing of gears you'll get metal fragments in the oil. Just clean them off the magnetic plug before refitting...
...a loose flex disc could cause a lot of trouble but the only way to check is to remove the gearbox from the car and measure the shaft end play. This is hard to do 'cos there's a spring and shims in the middle of the the output shaft that kind of floats up against the input shaft. If the output shaft (with the yoke fitted) has any obvious play in it then I'd be tempted not to risk it but remove and check.
The torque for the output shaft nut is 160Nm == 118 ft lbs
You could try ATF as an alternative for the gearbox oil. Dexron II if you can find it where you live. These gearboxes are pretty fussy. That is the cheapest thing to do other than doing nothing (which might end up being more expensive if you see what I mean).
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