I've completed the main quest and slain the "mad god", but when I return to the city to update the king, he keeps asking me to investigate the fabricant attack on the city. It seems stuck there and I can't tell him of the events in the Clockwork City.

Is there a code to get past that quest so I can update him on the final quest?

(Edit)

And as an afterthought, is there anywhere else in Morrowind you can use the Dwemer Satchel charges beside the two quest uses?

Far as I remeber you get a topic update when you go down the ladder and sit and wait in the hole in the wall, looking out over the chamber where the fabricants and the dwemer constructs are fighting.
Because once you jump down you cant really get back up again, to report to king Helseth or the tribunal dude(what was he called?)

I went back up there purely because I thought I would need a lot more potions, reported to the king and got sent back in. But I dont suppose you want to schlep through the whole clockwork city again. Have you tried speaking to some of the other characters to try and move the story along?

Sorry I'm not much help on the console commands though, you could google it or search this site for console commands