New guitar difficult to play?

I recently picked up a new Yamaha FSX3, but I’m finding it harder to play than my old Fender. Barre chords hurt and result in muted strings, especially near the top and bottom of the fret board. The store adjusted the truss rod but I think it still needs some tweaking. Anything else I should try? Maybe different strings? (They’re currently Elixir NANOWEB 80/20 Bronze Light). Or should I let a technician sand down the nut/bridge? Maybe I simply need to get used to it. Any help is appreciated.