It's easier now, been there done that,
MS 1 or MS II is the CPU type (depending on what code you going to run as well I believe), I'm using MS II on the v3.0 board over the older v2.2 board, the v3.0 can support direct drivers, which I'm not using, but I believe you can control the coil(s) directly from the v3.0 board, the 2.2 board had to have extra hardware (fly back board I believe) .
when I did mine, I just uses MS for fuel, running the original dissy, then later I set-up waste spark, but the instructions (manual), are well done, easy step by step (as long as you know what you want). the actual first time set-up was a little over wheeling, but if you go through the manual it has answers for 95% of what you need. it would also help if it wasn't your Daily Drive, so you don't stress out if it's not doing what you want it to do.
Nigel