Sounds like you're doing everything right so far. The cut ends of the housings should be flared enough to eliminate any possible friction from burrs. All of the cable needs to be out of the shifter at the time you attach the cable to the derailleur. I see no reason you can't flip the housing around to move the inline barrel adjuster as long as there is enough space around the barrel adjuster, but I've never worked with an inline adjuster. I wouldn't worry about the amount of cable pull you can see at this point. Everything needs to be in place to realize the correct cable pull. Be sure your handlebar bag does not cause any bends in the shift cables. This use to be a big problem with Backroads' touring bicycles equipped with STI.

Al