Make sure your DPI is maximised on the mouse and that all of the Naga bindings are set to their native defaults in Synapse. Synapse settings like bindings do not store correctly on-board Razer mice, but DPI, polling and lighting does.
Tap the DPI up button a few times while connected to Xim and double-check that the DPI has stuck to the mouse. You can do this by forcing a save in Synapse using the Sensitivity Stages tab.
Also note that you have no control over the stages, the mouse uses the factory defaults when not connected to Synapse (e.g 12.5%, 25%, 50%, 75%, 100% max DPI), hence the need to hit DPI up a few times to get to the max DPI.
At 8200 DPI, Xim sensitivity for HIP should be in the region of 20-25 for HIP and 15-20 for ADS. If your Naga is really slow at that sensitivity, hit the DPI button on the mouse. Also check that in-game sensitivity is maxed. Once you've nailed all that down, it's also worth tuning your mouse surface correctly.
If you still have pixel-skipping and frame-jumping, it could be your sensitivity is set way too high (and ultimately slowing the mouse down), the mouse needs more power (I've had a dozen Razer mice and none worked properly on a Xim without a powered USB hub) or the sensor just plain sucks (true of almost all Razer mice).
An alternative and better mouse for Xim would be the Logitech G502 if you need a lot of buttons. After suffering 5+ years of Razer mice on three generations of Xim, I swapped to a Logitech G303 a year or so ago and never looked back. Anything with a Pixart PMW 3310, 3360, 3366 or newer sensor is a perfect match for Xim and I can't recommend the recent Logitechs highly enough.
Finally, be a little bit careful with your Stinky bindings. Modifier keys like Ctrl, Alt and Shift don't work (by design) and Stinky can prevent other keys from binding correctly in Xim Manager if plugged in at the time. I bind my Stinky to say 1,2,3,4 and use the kb to configure Xim Manager with those bindings. Once the bindings are saved, plug the Stinky in and the Xim will pick up it's presses as 1,2,3,4 and respond with the correct controller bindings. If you've bound Stinky to W,A,S,D then you've already got that covered
