[sjf911]

MS3 without MS3X is very similar to MS2 so not much tuning difference although larger tables. MS3X adds sequential control as well as a host of input and output ports which adds a lot of wiring. Also, with MS3X comes a lot of other things that are easier to implement compared to MS2/MS3 such as open/closed loop idle control, AC control, open/closed loop boost control, fan control, launch control, etc., some of which require a lot of closed loop tuning. You also get vehicle speed and gear specific functions and a lot of user settable items.
I am currently running full sequential injection/ignition with 12 LS2 D585 coils in a CNP twin-plug setup. I am only running open loop warm-up idle control right now with a 3-wire Bosch valve that is stock to the 3.2 but have played with closed loop tuning which I will ultimately migrate to to allow AC idle up and load dependent AC shutoff (I pre-wired the AC system with this in mind). I log all of the normal engine parameters as well as pre and post IC intake temps, vehicle speed, gear selection, mass air flow (with a Ford blade style MAF between the IC and throttle body), and methanol injector flow via a CoolingMist injection controller with in-line flow sensor. I have a manual boost controller but this system can be used to do electronic boost control with the addition of an appropriate PWM valve which I have pre-wired for but not hooked up. This would allow for significant failsafe operations based on EGT, O2, or knock feedback. You could also control water/methanol injection with this setup.