As a first step, make sure the tracking is set up optimally and you've done everything possible to improve it. Also, make sure the Oculus LEDs are not getting power as they may interfere with tracking the Phasespace LEDs.
Swapping markers might be difficult to get a good result with. If you have a way to determine which tracker is getting reliable data then you could re-parent the viewpoint to that tracker in the main script. See the following example:
http://forum.worldviz.com/showthread.php?t=5260
You would also need to apply an offset to the left/right trackers to match the location of the front tracker.