One thing I noticed with Fireware 4 is in the AF sub menus the Release/Focus priority settings are both default set to release priority (ie for Single Point and for Continuous)
This means the camera is prioritising release over focus accuracy.
Might be worth checking this setting if you have not already as that might help with accuracy of focus.
+1 as well to using CL mode. I used to always use that on my X-E2 as on the X-E2 in CH mode it would not re-focus between frames, so even in C mode on the front dial when in CH it would focus for the firts shot and then lock at that focus for remaining shots.
I found that Cl was actually quite good for most applications good example my daughter going down a slide and running towards me, in CH mode I would get about 17 shots of which the first 4 or 5 were vaguely acceptable but nothing special. Same thing in CL mode I would only get 6 shots, but 5 of them were very sharpa nd one passable none were as badly focused as the CH mode. I would rather have less shots and them all be useable than lots of not very good shots. YMMV
Now the X-T1 does re-focus between shots, I think the shot rate does go down slightly if you have focus priority on, but its not as slow as CL, so I think that CH plus focus priority is probably the sweet spot, but I need to experiment more.
Most of the above was done with Single AF, not played with Zone AF and burst shooting yet. I have mainly be focusing on comparing it to X-E2 with a view to which camera I keep.