It really will shift better if you size big-big+4 as Sram recommends but probably not enough to explain your issues (except B tension--this is one of the reasons). The ferrule not seating into the shifter is quite likely to be causing problems. Also your new drivetrain setup is more sensitive to hanger alignment than your old, so I'd definitely make sure it is aligned precisely with a hanger alignment tool. Also did you seriously reuse housing on a new drivetrain installation? Waste of time--take care of it with the new installation to make sure that friction isn't the problem.
I hope you have the cut portion of your chain still, otherwise the odds of the shop insisting on a new one are high.