I haven't posted any updates for a little while, but have done lots! Made some significant changes to the schematics (and therefore the boards) after testing on breadboard (pictures to follow), and also about 80% complete on code.
Biggest problem right now is not the box, but the stuff that comes afterwards. I've been having problems getting the exposure time right, and even copper-etch. I believe this is due to the way the inkjet printer is printing on the film - it leaves a visible grid of tiny dots, which are being etched.
Here you can see the result of exposure. At first glance, looks pretty detailed (ignore the finger smudges), but the slight amount of green resist remaining in the middle (by the two parallel tracks) is enough to cause problems etching.
Here is the same board etched. Oddly, the board is over etched at the area where I expected it to be under-etched.
Here's another example. This one is showing massive exposure problems, simply due to light leaking through the ink on the acetate film. I have also tried using paper, and then oil to make it more transparent, but this is messy and absurdly inconsistent.
Conclusion? Inkjet might be a bust, unless you have a particular printer that prints very solid blacks. It's not just a cheap-printer problem, either - the Canon ip7200 I have is pretty decent, it just doesn't print on film that well.
I now have acquired a laser printer and tracing paper, so trying that. I also have some new chemicals, so will be trying Sodium Metasilicate Pentahydrate instead of Sodium Hydroxide.
There's a great detailed guide here: http://www.electricstuff.co.uk/pcbs.html