Hi Trig,
Ain't no elect guru... but enjoy fiddling. Also, am very much aware the Honda wiring can change over models etc... but most likely...
Your loom. The BLACK is likely a switched live... ie is 12V +ve @ all times the ignition is switched ON.
The green / yellow stripe is the switched feed to the brake light, with the switch being either the front or rear brake switches. So... black live into those switches... you brake.... and now the 12v continues down the green / yellow to the brake lamp... through this & completes the circuit to earth.
The electronic ignition needs a 12v supply.... and so you need to connect your loom BLACK to its BLACK. This BLACK elect ign feed is typically taken from the Honda rear brake switch which is the closest / easiest power take-off to the points plate. You need to disconnect the BLACK bullet connector to the rear brake switch, and insert a 'Y' feed, ie so the loom BLACK now supplies both the brake switch AND your electronic ignition. (this 'Y' feed wire is typically supplied with the electronic ignition kit - tho you can easily fabricate one assuming you have bullet connectors etc).
The GREEN / YELLOW simply connects as standard, ie the other wire out of the brake switch.
(the brake light switch has two wires, and nope, it doesn't matter which way 'round they're connected to the BLACK & GREEN / YELLOW loom connectors. What does matter is that the BLACK loom is used to feed the BLACK elect ign.)
Which leaves the electronic ignition BLUE & YELLOW.... and these are connected to the respective BLUE & YELLOW wires of the L & R coils.... which should be down in the points housing & previously connected to the deleted points.
This may be your system set-up.... expand the Instructions leaflet.
http://www.cmsnl.com/cb550k3-four-england_model14671/ignition-assyelectronic-kokusan_03020300505/Hope this all makes sense,
Simon.