For a plot point in my SR3 game I intend to have a permanent transmutation spell but I'm not sure what its stats should be. As far as I can tell from MitS the TN should equal the OR of the original material, (In this case at least 10) but I'm not sure about setting a threshold. Can anyone help?

im going to say the threshold should be the difference in the barrier rating of the material.

Difference in Barrier rating? I'm not sure I understand. Regadrdless this particular spell is intended to transmute a liquid so barrier rating is a little tricky.

Ah what the hell, can anyone put up stats for a 'Transmute High Grade nuclear waste to Enriched Uranium spell please?

As far as I figure its +1S for drain code but I need Threshold and quantity affected by force. I was considering (force)cf but since 1 cf is the amount produced per day by a typical plant it seems redundant to make more powerful versions.

Its a plot point, why bother stating it. Do you plan on giving the spell to the players as loot or something. This seems like a toxic shaman exclusive IMO. If you want a threshold, make it X+1 per KG of material. X being whatever the OR threshold is for stuff like toxic waste in 3e. For a toxic shaman I'd let them reduce the threshold by there power rating.

I want to be sure that the Hermetic wage-mage I'm building as an NPC is actually capable of getting the spell to work reliably. Not sure why you think it would be a Toxic spell, it's specifically designed to reclaim waste and turn it into something usable.
I don't think the threshold should be linked to OR as thats the TN for the spell anyway, to base the threshold on it feels like double dipping and would make the spell damn near impossible to cast effectively (TN 10, 10 successes required)