Thanks Jye, your photos were a great help.
At first I couldn't work out why the fan wouldn't turn the magnet. The fan would start to spin but would just sit there and quiver. I think the magnet was interfering with the motor, so I stuck a 3/8" washer under it which made it go. I guess my fan didn't have a metal bit under the centre like some pics i've seen.
I was a bit lucky when I glued it all in, I must have got it almost centered. If I keep the speed low enough, the stirrer doesn't develop any precessional movement. I reckon if I want higher speed i'll have to raise the fan up a bit inside the case with some spacers. I should be OK without it though.
I ran it non-stop overnight in the 2l flask and it was still running happily this morning, with no signs of overheating. Now I just need to wait for the wyeast order to come in.