Wrt to the PDFs, you could print to PDF with something like primo PDF.
About the routing, you've managed to route a pretty complex circuit on just two layers which is awesome but I think the sacrifice is a proper ground plane. The core concept is that, all analog (and digital) signals are a measurement of voltage with respect to ground. Now if there are currents flowing on the ground trace and its impedance is not very close to 0 ohms, there will be some drop which will cause error. High speed digital circuits are particularly troublesome because it doesn't require much capacitance for them to couple to other traces and also if there isn't a low INDUCTANCE gnd return, there will be a high impedance return path and hence a lot of drop inducing error. Inductance is really synonymous with loop area (and a lot of other things but area is a good simplification). So if you we're to trace the path of where the return currents were flowing for say u201 and the LCD, in the first rev of your board, they go along the same path so that is big trouble. The loop area of the path is also very large so the impact is even worse.
Unfortunately I think that the best solution is to start routing from scratch, take all of the parts in you schematic and classify them as either analog or digital. Of course your uc is mixed signal so it is in both domains. I would then use the top of the board for all analog components, place the uc in the middle of the board then the LCD at the bottom as far away as possible from the analog. Your power supplies are in a good place already. Then try to route ALL signals on the top layer. If that isn't possible, use very short links on the bottom layer to cross over the top traces. Then when everything is routed pour the bottom with as much ground as you can. This will perform much much better. Since you don't have a power supply plane, it is also very important to decouple VCC pins very well so that the traces source dc current only and high freq current is sourced from the cap. If possible, one cap per pin but that isn't always reasonable so try your best. Also when place visa on these caps, you should do it in a low inductance manor, just google it and you'll get a ton of hits. Use of ferries is a good supplement too but it isn't as important as the other stuff.
Always, the best layout starts with smart design partitioning, logical placement of components, optimize for low inductance routing and maintain as continuous of a ground plane as possible. Caps are cheap too. I always think it is better to solve EMI with low gnd impedance paths. One other supplement would be some series resistors on your dpi bus especially the clk.
Good luck!