Conduit can look quite nice, and it's available pre-painted. A simple matte black finish tends to make metal look 'clean.'
You job is complicated, however, by the uneven faces of the logs. This means either you use Mineralacs to space the pipe off the surface (not a bad idea, as it allows for cleaning), or you rout a groove in the face of the logs.
For routing, there is one word: Festo. Quite expensive, the Festo system includes rails that will guide the router independent of the surface of the logs. IMO, a good bed of caulk will suffice to support the pipe; boxes can be screwed to the logs.
Even with the fanciest arrangement, you'll still have plenty of hand & chisel work, especially at fittings and bends.
For drilling holes, nothing beats an impact driver. The 1/4" hex collet models will make holes to about 1" diameter; Both Milwaukee and Makita make larger models that have a 7/16" hex collet, and will take the 'self -feed' bits for larger holes.
