I can regularly get within .005", and often .003" or better. To do that, everything has to be dialed in just right and maintained, and you also have to calibrate and maintain calibration.
It sounds like you've hit most of the possible causes of lost steps, but here's a few things to consider:
1. Belt tension-Too tight and the motors have to work hard, you lose steps. Too loose, and there's slop. How are you measuring belt tension?
2. Potentiometers-Have you adjusted your pots? Too low and motors don't get the power they need, too high and they thermally overload.
3. V-wheels-Yeah, these are hard to quantify. I typically set mine so I can put 2 fingers on opposite sides of the wheel (across the diameter), and if they're fairly easy to spin without a lot of force they're good. Easily spinning them with 1 finger is too loose.
4. Pulleys-One of the screws needs to be seated snugly down in the center of the flat. Loctite (blue) is recommended.
5. Modifications-If you stiffened the X and Y axes, your pockets will be consistently deeper and your axes stiffer. If not, you may have some twist/flex issues. This is especially probable if you have a heavy router and a non-stiffened X axis.
There's quite a few more things, but those are the most common issues. Here's a couple threads I've started that you may be interested in:
It takes some work, and some things seem counterintuitive, but once you get it dialed in you'll be getting .005" accuracy.