yeah.... that's how alot of megasquirt is.My suggestions study study study, read more, study more, build your unit, build a tune for it, test it on the stimulator, wire it into the car, test and repeat. Once you got the engine started, start playing with the tune.
http://www.megamanual.com/index.html - this is your new best friend.
http://diyautotune.com/ these guys are awesome, it's where i got my kit from.
I spent about 3 months studying the megamanual and playing with megatune before i even got my megasquirt. Then i built it, played with it for another week doing all the testing. In ~4 hours i wired it into my car, I actually got it to start the third time cranking it. Stock KA at that point, it ran rich but i was just playing around. Over this winter i built my turbo kit, retuned for 555cc injectors and have been having fun with it ever since. This time around, car fired right up the first time, and other then being overly rich under boost (initially) everything runs awesome.
I can help with the tuning and building. I think for the coilpacks though your going to have to run 4 separate coil controls, as well as getting some type of wheel setup. Just read alot and i'm sure you'll find the answers. I know someone on the megasquirt forums has done it before.