The copper is covered with solder-mask, a sort of resin. You need to scrape it off, or use sharp pointed probes.
It appears that I should solve for odd characteristic impedances of 50 Ohms each. Is this true?
Yes, the differential-mode impedance is equal to twice the odd-mode impedance (at least for symmetric geometries).
My board house can do 5/5 mil trace/space. Is there any reason not to use these values?
If you can fit a design with larger gaps and wider traces, then the differential impedance will be less sensitive to over-etching or under-etching during pcb fabrication.
How much of an effect will soldermask have on the circuit? Should I keep the differential traces uncovered?
Is a fairly small effect. But if you can, it's worth checking the geometry with a simulator that can account for the effect. Your fab shop may be able to do this for you, if they aren't a totally low-cost shop.
Leaving the traces unmasked is also an option. But remember to leave a sliver of solder mask around each component pad to act as a solder dam.
If you are using a higher-end fab shop, you can also simply specify that you want 100-ohm differential traces, and let them adjust the trace width according to their knowledge of the material characteristics, solder mask thickness, trace thickness, etc.
Best Answer
Cladding is the copper layer applied to the surface of a board substrate: it's the starting material. This layer is selectively etched away to form traces in the finished PCB.