[sjf911]

I started with MS2 then upgraded to MS3 followed by the addition of MS3X when it became available. MS3/MS3X offers a huge amount of flexibility over MS2 but comes at the cost of complexity and an OS that is still being developed. Neither provide adequate knock provisions but the MS3/X lends itself to use of the J&S for COP or CNP knock control.
Going to sequential injection/ignition where the MS3 really shines requires adding a cam sensor which is not impossible DIY by modifying the air pump drive or the distributor but probably easiest done with Clewett's combined scavenge pump/cam sensor unit which is not cheap. Converting to the 964/993 oil filter and using the right hand cam for the standard sensor is also possible.
You need to decide what level of control you want and let that dictate which system you get. You can get >90% from MS2 with a lot less build hassle. DIYAutotune is one of the main sources for components but BoostEngineering is useful for Ford EDIS components if you go that direction in ignition and Clewett is indispensable. I am running Clewett crank and cam sensors with his crank pulley/60-2 wheel combination. The MS3/X ECU is from DIY as is the MS2 harness. I had to add an additional harness for the MS3X but made that myself although it would be cheaper to get one from DIY now that they are available. IIRC, I sourced my LC-1 from DIY as well.
Base tunes are going to vary from car to car so much that I wouldn't start with someone else's tune, except for conservative timing. Dyno time is really helpful especially to confirm timing and the accuracy of your wide-band O2 controller which you will very heavily rely on for tuning.