I ran into the same problem with the Microtouch/FocusMax set-up on my refractor.
I found that it was necessary to trick Sequence into moving the focus by the right distances.
I measured how many steps the Microtouch needed to move 1mm. In my case it moved 72mm for 20,000 steps, ie 0.36mm per 100steps.
I then established that Sequence thinks 100 Microtouch steps is 0.1mm, so that I had to set the coarse and fine AF steps in Sequence to 1/3.6 times the actual value I wanted.
Using this as a starting point, I then altered the steps until I got the right HFD shifts for coarse and fine shifts.
This has given satisfactory AF performance during Sequence runs.
With the focus offsets, I just used what Sequence AF measured, and it worked OK.
Hope this helps!
Edited by MarkS, 14 September 2016 - 01:58 AM.