I am not a Vbar expert, but I would say you need to ensure your servos are throwing the correct direction first, before you start worrying about leveling the swash. I think that's actually the first step in the setup wizard as well. Once you have them throwing in the correct orientation, then you can make sure you have the horns on at 90*. You should only have to use the slightest amount of subtrim in the Vbar setup wizard in order to get everything level, especially if you bought Ralph's titanium pitch links along with your swash tool.
Following Chris' setup videos, I oriented my servos before I placed them on the airframe to make sure I had the horns on as close to 90* as possible, then started the Vbar setup as normal. I only had to move one of the horns up one or two splines to get it almost perfect, and I only needed about two or three clicks of the mouse on the subtrim swash leveling step to get the plate level.
Make sure you are doing all of this at mid stick as well, or it's pointless. Check out Mr. Mel's setup videos if you haven't done so already.