pkoteras,
Firstly - welcome to the forum.
Secondly - send me a Personel Mail with your email address, and I'll send you a document that will help you understand the electrics a little better.
Now, to a few explanatory points.
The bike you have is a positive earth system, so please be careful not to confuse yourself with polarities.
The Micro MKIII is a Boyer Bransden ignition system - lots of good info on their site
http://www.boyerbransden.com/
The Boyer has two basic sections - the black box "ignition amplifier" and the pickup unit. The pickup unit consist of two coils mounted on a circuit board, and fitted where the points used to go in the timing cover (behind the 3" round cover RHS lower engine casing). Also in there is a rotating plate fitted with two magnets to "signal" the amplifier unit to spark. The black box switches the battery -ve to the coils (coils wired in series), but only switches it on after the first pulse is received from the pickup. It turns it off after about 3 seconds of no pulses - saves coils getting burnt out and battery life. Both coils/plugs fire at the same time, so you get a spark every revolution.
You cannot take the black box out without also changing the pickup unit for the original points plate and auto-advance cam system, and adding back in the condensors.
Put the Boyer back in - if you can't remember how it went, the Boyer site has the wiring diagram - Kit 52 for your bike. Check the continuity of the pickup coils - under 700 ohms from where the two leads connect to the Boyer box - black/yellow stripe and black/white stripe.
with everything turn off, check for resistance between black lead of Boyer and earth (coils primary windings) - should be between 7 and 9 ohms for 2 x 12 v coils, or 3-4 for 2 x 6V coils.
With ign on, and plugs removed and placed on the head fins (still connected to leads of course) measure for 12V between battery +ve and the -ve of the first coil connected to the Boyer black lead, after kicking once. Beware that there can be up to 400V pulsed on this terminal, so don't get your fingers in the way.
Let us know what you find.
Pete