The versions of MS can indeed be confusing. But it's not as bad as it seems if you eliminate a few things from the start.
MS1 - Old hat now (even though I wrote a lot of the code) forget this version unless you want a setup thats very basic. MS2 is another £50, its welkl worth that small cost!
MS2 - This is the ideal setup as its very tuneable, easier than MS1 to get your head around and it has a better backup these days due to more people having it.
MS3 - This is similar to MS2 except it has SD datalogging and USB connection (MS1 and MS2 can both have USB) Its main advantage is being able to control a V8, etc, in a sequential mode. To acheive seq fuel and spark its a lot more cash than MS2 (£150 plus the COPs,etc)
But having said the above, if you get the V3.0 pcb then you can upgrade from MS1 to MS2 or to MS3, so its not like you make a decision and your stuck with it. Most people dont use MS1 these days, I would guess 5% of my sales are MS1 and thats for basic setups (generators, etc)
Have a look here for more info on boards, etc:
http://www.extraefi.co.uk/information_OL.htm
As for EDIS or direct fire, I personally prefer direct fire, again EDIS is old hat now and although its robust, your using second hand parts. I've had just as many issues with EDIS setups as I have with direct fire. The EDIS setups are harder to diagnose, where as direct fire setups are usually easier as long as the install is done well (grounds on engine, etc)
Direct fire setups mean you arent stuck to the Ford coils (even though they are very good) but you can use the RV8 coils as they are neater.
EDIS is also harder to wire in as theres another module to wire in and it takes up more room.
As for COPs, well I prefer them as the install is neater. Especially when you use the LS2 COPs with built in ignitors. They can sit on the rocker covers with a 3" HT lead to the plugs. But it is harder to install, as theres a lot more wires
But theres no power gains over any of them, an EDIS will produce the same engine power as a direct fire or a seq COP setup, so at the end of the day its your choice. Its like asking what colour car is best, its your preference,
Phil