Hi Ben,
Those are some good points on why the rear derailleur may be getting hung up now. I think you may be right in that I disturbed the derailleur housing where it goes into the lever. I will check that when I get home today
As for my rear brake I had clean cuts on the housing and ground the ends smooth using my angle grinder. I will check the lever for smoothness under no cable load. I do have a feeling it may be something in the top tube. The bike has an internal sleeve in the carbon fiber top tube so I didn't have to do any cable fishing. I have had the thought that maybe they screwed up this internal tub when they cast the carbon frame but am not sure. I am also not sure if this internal tubing is removable or replaceable which has me worried.