Whew, that was an intense couple of hours... but the board is now more or less done. Unfortunately the addition of the 'jumpers' has destroyed the neatness and covered most of the components in a couple of layers of wire... which means that any debugging is going to be a challenge.
These jumpers are basically of two types. They either take one of the supply voltages to a piece of the circuit that needs it or they consolidate the leads to and from the external components into a central spot to reduce spaghetti in the assembled pedal.
There are a couple of things that I could have done to make the power wires a bit neater. Firstly, I could have given each of the voltages its own rail running the length of the board (I did this with +4.5V and ground)... but this would have required an additional 3 rails. Secondly (assuming I did the first) I could have given those jumpers the same weight as a component during the layout phase, ensuring they could run in straight lines and not cross any components... but this would have added a good few additional rows. In other words to do it properly I would need a bigger box.
The leads for the external components are a little more tricky. If I didn't consolidate them then the board itself would be a lot cleaner, but the box would be unmanageable (that might be preferable... this is my first pedal... I don't really know). I can think of a few other options (such as an intermediate board) but they all require significantly more space.
... but that's all theoretical. This is what I've built... it looks like it's going to fit and right now all I can do is hold thumbs and hope it works first time (lol) because the other option is too horrifying to contemplate. ?