>but the engine oil is still a pristine green (on the dipstick) and 
>the stuff being dropped is black. Could this be clean engine oil 
>picking up clutch dust on the way out (would surely lead to clutch
>slip?) or is it more likely to be from the gearbox?

I understand your hesitation at pulling the new engine, but it really is
the first step and the only way that you will know what is happening.

Is the oil very viscous and with a different smell than engine oil?
If so, indicates transaxle oil.

Get to work, and good luck,

Wolf