Let me see if I can help you straighten this mess out. Lol. Are you working on a pre-2003 Blasty? These years of the quad, like the one in your sig, have two 'Black Boxes' under the cover. One controls the TORS. The other is your CDI box.
Assuming that you have a PRE-2003 Blaster with separate TORS/CDI boxes, the green wire has nothing to do with the ignition system. It simply supplies current to the low oil level switch that used to be inside the oil tank. You can cut/remove this wire, as well as the black wire running alongside it. This won't affect the running of the engine. Connections like these VV are used by Yamaha to tie like circuits together.
All the solid black wires you see inside the harness are ground wires. The black wire that used to go to the oil switch is simply an un-needed ground that can be cut at the factory splice. On these Blasters (88-'02), the CDI box is the one mounted lower on the front frame. There are four wires entering the box from the stator, and one more orange wire leaving the box to go to the ignition coil. See pic VV.
Just connect the four wires coming from the stator to the CDI box VV
and the quad will run, provided that the TORS 'Black Box' has been removed. You can cut all the TORS wiring out of the harness without hurting anything. Snip out all the yellows, and then go for the black grounds at their splices. With the TORS all removed and the four CDI leads hooked up, the engine will start and run fine. I:I
I will say that later model Blasters (2003-on) use one, unitized CDI and TORS box under the front cover. On these quads, or if you are using a post-2003 stator plate on a pre-2003 wiring harness, there WILL be a green wire coming right off the stator plate. You will need to ground it out for the engine to run. You can still cut all the TORS and low oil level switch wiring (including the green one) out of the bike; just remember to ground the green stator wire out against the frame, or the engine won't start.
Good Luck!