This one came out much better.
I moved two connectors so that they lined up better, then made the signal lines slightly thinner. This time the board auto-routed without me needing to manually route any lines. I then moved some of the tracks to be horizontal/vertical instead of diagonal, and I moved some of the marginal lines further apart.
When I plotted it only one pad was too close to another, but the SO08 pads still, as expected, merged and will need manual rework with a knife.
Here is the original.
And here is the annotated version.
1. Same as before these two pads should be separate.
2. These two should not be so close.
So the next step is to do that and then etch the board.