Are you sure the cable housings sit perfectly in the exits from the brake lever? Can you easily slide the cable from the lever side when disconnected from the brake and lulled out of the rear housing? Likewise the derailleur cable. (Having never owned a brifter, I do not know if accessing the cable at the shifter is possible.)

I write this and I just thought - is your rear brake cable full length? If so the trouble-shooting I am suggesting is going to be a lot less definitive. Maybe pull the entire housing out of the frame and do my test above. Then you would know if the issue is at your lever/HB tape or perhaps too sharp a turn inside your frame.

If it is inside your frame and you have bare cable there, is it possible that it is contacting some carbon fiber that wasn't properly pressed into place when the frame was made? That would explain the rough feeling. You could try running the brake cable in a full housing run on top of the top tube, tying it in place with wiring ties. (Except for the wiring ties instead of braze-ons., what all steel bikes of the '80s had.)

Edit: re: the shifting - could you have disturbed the housing exit from the lever when you re-taped the bars?

Ben