I recently acquired both a wraithlord and a wraithseer kit. In an effort to make them very visually distinct, I'll be converting them both fairly heavily. I've begun work on the Wraithlord. He shall be named William.
Here's the page of notes and sketches that I put together to help me organize my thoughts. It's by no means comprehensive, but it'll provide me with a good starting point.
I began by assembling (mostly) the torso sub-assembly. One of the most notable differences between Willy and the as-yet unnamed seer will be detail. Willy will be a trimmed down fighting machine, designed for efficient destruction, while The seer will have some more ornamentation. As such, the collar piece will be ditched for a sleeker looking neck.
Another distinguishing feature will be the number of warp vanes present. The seer, with the need to draw extra energy from the warp, will have two vanes, whereas Willy will have a single, centrally located vane (is...that what warp vanes are for? It is, right?). To ensure that he won't be stuck without enough power at a critical moment (and to fill some visual space), he'll have two warp batteries installed where the little holes are.
Both William and the seer will have necks, because it's an atrocious waste to design such a graceful vehicle and then put it's head right on it's shoulders. C'mon, GW, get your crap together.
Another key difference between the models will be the legs. The seer will use the stock legs, unaltered aside from probable reposing, while Will's legs will be altered to visually relate to the Eldar war walkers--they'll be digitigrade, like a bird's foot, and will use the hoof-like foot from the seer kit. The seer will use the more humanoid feet from the wraithlord kit.
My next steps will be finishing the parts I've started and building a base, I think.