Indexing was my thought for 2 layer boards.
- Set up your stand-off holes in each corner of your PCB design.
- Do everything to get the top layer toner transferred onto the PCB or just stick the top sheet in place (heat resistant clear tape?).
- Drill pilot holes through the board at te centre of each stand-off. Size to be for a 0.1" male header.
- Print off the bottom layer.
- Place bottom layer print onto a block of wood and drill the same 4 pilot holes though the paper/vinyl/laminate.
- Place 4 off 1x1 headers through the PCB from top layer and turn the board upside down.
- Place your bottom layer print over the 4 keys to line up perfectly via the centres of the stand-offs.
- Stick the bottom layer in place (heat resistant clear tape?).
- Heat transfer the toner onto the copper via heat press, iron or laminator.
- Remove both sheets of paper/vinyl/laminate and the 4 off 1x1 headers used as keys.
- Etch
- Hopefully a perfectly aligned two layers.
I've not tried it yet but I think it should work?