Many thanks for the replies.
I set the timing 35-36 deg advanced with the ATD wedged, and I checked it after everything was tight, so I don't think it's that.
I get a good spark, so the mag seems ok. When looking at the mag from the primary case side I've got the left lead going to the left cylinder, which is how it was when I took it off.
I noticed that after I'd done up the ATD bolt with a new C washer and took the wedge out I had to manually push the ATD back to the non-advanced position. The springs couldn't do it, which seemed wrong to me?