After staring at my reference material for what felt like days, I eventually settled on a close-up of a few in-game screenshots I took as being the best guide. Having printed out a few images, I then proceeded to sketch in the lines directly on the model itself.
Next came the really tricky part: Having drawn the lines in, I very carefully and gently scored the lines into the wood using a variety of sharp metal objects. The tip of a nail seemed to give the best results. I then wiped the excess pencil marks off with a damp cloth, leaving very narrow grooves slightly darkened with pencil markings. This gives quite a good impression of fine panel lines.
Of course some minor damage is caused to the outer paint layer, but nothing that cannot be touched up later. Adding this detail also had the unexpected side effect of giving the ship a slightly used and weathered look, which is exactly want you want for that extra bit of authenticity.
Here is a final look at my progress thus far. I think it has turned out quite well! I've covered just about the whole ship; let me know what you think!