Is there a way to stop the tracking or refining process and re align joycon motion controllers to the correct axis? I understand the joycons aren't as accurate as the the move controllers but they're what I currently have access to.

If I keep sudden movements to a minimum they seem to do reasonably well on my hands, however the one on my head starts drifting almost immediately, but often it will maintain its new orientation for quite a while. it would be nice to be able to manually rotate the controller during the tracking process.

You normally perform tracking before applying motion data from controllers. So there is no need to do corrections during tracking.
When applying motion data, you can try to compensate for drifting by processing in smaller regions of frames. E.g. set a small ROI where you think motion data is stable enough, adjust a bone's position in one of the frames and apply motion data - it only affects the selected ROI. Then set another ROI and repeat.

I think I did it correctly - the mocap from dual Azure Kinects was tracked and seemed fine. Then, in an attempt to add wrist rotation, I aligned the 1200Mhz PS moves to the 2nd Kinect camera which you can see here:
https://1drv.ms/u/s!Arg1GuG9JW4eh9Mzy-JTIRgTHg5j5A?e=ZhexBA

But not more than 60 frames later it was out of alignment already. I bought these PS moves because I thought their higher refresh rate was supposed to mitigate the amount of drift, but they almost seem worse than the Nintendo joycons.
https://1drv.ms/u/s!Arg1GuG9JW4eh9M0s2BY8uleWZpo_A?e=Dw9n1F

Since the wrist WAS fine before I applied the motion controller data - what am I supposed to do to fix the drift?

Are you sure you properly matched controllers with body parts in Mocap Studio?
Can you share an iPiVideo file?

Here is a video and iPiMotion file:
https://1drv.ms/u/s!Arg1GuG9JW4eh9M4rYHP8pJCkfHoOw?e=9lDxCL

Hi
I've looked at your video.

One thing I've noticed first is when you are "aiming" at a camera, you hold a controller not the way we recommend. So it is hard to use the "Align with camera" function in Mocap Studio. The sphere part should be the closest to a camera. See a sample picture in the docs:
https://docs.ipisoft.com/Motion_Controllers#Tips_on_action_video

Nevertheless, it looks like there's some inconsistency in motion data from the hand controller #2 and I could not get well-captured rotation of the hand throughout the whole video. On the other hand (no pun intended), the head controller #1 looks good enough to me. So there is a probability you get bad data from one of the controllers. Either because the controller itself is faulty. Or because your BT adapter does not cope well with two controllers. Or (less likely) because of poor calibration in iPi Recorder.

• Try to re-calibrate controllers in Recorder.
• Try to use just a single controller (each of them) during recording to see if that helps.
• Try to move the BT adapter closer to the capture area. With the PC itself or using an USB extension cable.
• In case you're using a built-in BT, try getting an external one with extended operation range (10m+).

I had tried holding it the suggested way in an earlier test and actually got worse results - so you may be right about bad data from the blue tooth controller or the ps move. I will try using a different BT controller with just that device and see if it helps.