Yes, you can fuel and time each cylinder differently if you are setup for sequential. Sequential requires a cam sensor. I use a Jeep 4.0 cam sensor with an adapter from SD concepts and Andy F's awesome Billet 36-1 trigger wheel.

You have your base fuel table and timing tables, from there you can add or subtract a % of fuel from each cylinder. I have not messed with per cylinder timing but I assume it works the same way.

MS3X can even run closed loop per cylinder if you happen to have 8 02 sensors.