There's three main boards currently on the market (not counting the eMS-Pro) and two processors.
The V2.2 is sort of the base model. It's designed for fuel only control with high impedance injectors, but can be expanded to work with other things.
The V3.0 adds some ignition control features, including the ability to read variable reluctor sensors and a lot more overcurrent protection.
The V3.57 only comes in assembled form. It's basically a surface mount V3.0, although it has an extra connector that is handy for six coil ignition systems.
The Megasquirt-I processor is an older design, with more documentation and testing for extra I/O functions. The Megasquirt-II has a faster processor, but the distributorless ignition options aren't as well tested.
Right now, only the MS-I can drive six coils independantly.
To meet your desire for COP ignition, a Megasquirt-I with a V3.0 board (if you're building it yourself) or V3.57 (if you're buying one ready made) would be best.
You'll need some sort of trigger wheel setup, as the stock trigger wheel doesn't work for wasted spark. There's a couple options:
1. Use a crank trigger and fill in all but one hole on a ZXT optical distributor.
2. Machine a custom plate for the ZXT optical distributor that will let you use the Megasquirt's missing tooth wheel. Something like a 12-1 or 36-1 wheel will work.
Any amount your injectors can work with.
Almost anything with the V3.0 and higher boards, but there are a few limits. Just don't grab them off something truly weird, like a Bosch CIS K-Jetronic or a common rail diesel, and you should be all right.
Megasquirt-I can do this with a suitable trigger. Megasquirt-II is limited to four coil outputs, so you would need wasted spark.
Again, as long as it's not something too weird, yes. You'll need to figure out its dwell settings.