two cdis, you'll find that one is a rectifier regulator, this is from when it had the battery setup (can tell that it had a battery setup, by your stator pics and where the starter motor used to be etc). so what i would do is completey remove the rectifier and that will simplify your wire setup. You will then be able to make a nice neat wiring loom setup, with nice neat plugs etc (reason for nice neat plugs etc is so that if you need to work on your bike in the future, you can simply unplug certain components of the loom e.g remove cdi, kill, coil, stator seperately to one another, instead of having everything soldered and done up into one unit) but make sure you have some nice waterproof plugs or make them waterproof