So I have the same problem, only I have mistakenly taken the front side of the robot as the back side ;( So now front side of my robot faces -y axis.
I have the base_footprint joint origin yaw as +90 degrees, so front of my robot now faces +x axis. In addition I switched right and left wheels convention (since it is a diff drive robot), so used to be left wheels are now right and vice versa. Also the wheels' joint axis needed to be the negative sign, so that forward command actually drives the robot forward.
My related question is that could having this set up create problems later when navigation stack etc etc are included for navigating my robot?