Double sided board fail

Creating double-sided PCBs using toner transfer is never easy.
Getting both sides lined up exactly, while etching one side and protecting the other during the first part etch is a real pain in arse. At best, you can hope for boards that are "basically useable" but very rarely (only twice in my experience of making PCBs over about a hundred years I think) do you get a "perfect" board.

But this time, we've had a spectacular fail.

It's probably related to the Inkscape printing fail earlier, because this time not only did the two sides not line up (we could live with that at put it down to ham-fisted sausage fingers) but they're not even the right size!

Here's the first side of the board. Compared to the actual 16-pin soic component, it's the perfect size

(using the ExpressPCB-to-PDF-to-Inkscape-to-PNG-to-DTP-to-printer method, finally managed to get the pcb design onto the copper board via cheap chinese press-n-peel alternative (the bad etch in the far corner is where the board was handled before it went into the ferric chloride - d'oh!)

But on the reverse....

The print just about lines up with the first set of holes. Not perfect, but useable.
But by the time we get to the other end of a 100mm long PCB:

(the bad trace leading to the first hole is where I wiped the board with my wet finger to see if the print was misaligned, or just some debris on the board. It turns out it wasn't crud on the board!)

Not even close!
Frustratingly, the offset between the holes and the printout aren't even the same distance apart. So if the whole image was shift (as you look at the image above) slightly from the right to the left, then the holes at the other end (in the image before the one immediately above) would be too far out the other way.

If the whole thing was shifted, there's no way we can see of making this a "perfect" match. It's almost like the image needs to be printed at 101% to space the holes further apart.

Of course, it's not just these holes we need lining up. Throughout the board are much smaller, 0.5mm holes, to act as vias (in the event of a perfect line-up, or even a "good-enough" match we would normally just solder wires through these instead of messing about trying to plate through from one side to the other).

There's no way we'll be able to get our double-sided board working if this is as close as the two sides line up! So is the problem with Inkscrape, converting pdf to bitmap, or something else? Maybe one of the BuildBrighton lot have some ideas about double-sided boards........