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Ok here goes.
Picture A, ???1 , Kill switch wire(red/white) runs to blk/white wire coming from key switch. Tested and confirmed. 2 wire connector ??4 : wires are grn and blue/faded yellow stripe.goes to a light bulb on the chrome cover under handle bars, has a red lens cover, I figure its the high beam indicator ?

Picture E, 3 wire connector : wires are grn(ground), Yellow , and Dark grn. Dark Green goes to R/R.

Picture F,This is a 2 wire connector : wires are grn(ground) and blue/faded yellow, can't find any plug to connect to.(unhooked as of now) This is the wire that I thought was putting out low voltage.My brother tested it and it has 12 volts with key on.Where to plug it in ?

Picture G, should go to R/R : wires are Dark grn , yellow , grn(ground) I have this plugged into 3 wire connector from stator. ??2 is this connector. ??3 comes from Carb. 2 wire connector : wires are grn(ground) and Yellow. There is a 2 wire Female connector that also has grn(ground) wire and a yellow wire. I have these plugged into the carb. I believe this to be the auto choke ?

My brother tested the coil via how to test a coil off the internet and says its bad. I have a new one ordered and should be here Tueday.

This is how the wires are connected as of right now. Still no fire, hopfully new coil will fix.
The two wire connector from stator is pluigged into the CDI 2 wire connector.
The white/red female bullet connector from the engine plugs into the red/white male bullet connector from the CDI.
black/white on the CDI plugs into the black/yellow on the coil.
black on the CDI to black on coil.
3 wire plug from Stator(Picture G, should go to R/R) is plugged into the 3 wire plug from harness(Picture E)
Orange wire from CDI is plugged into red/white from harness which goes to blk/white wire from key switch.

After I get this beast running, I want to put no rev limit CDI on it.(Yamaha JOG Zuma Minarelli 1E40QMB performance race ignition CDI) from ScrappDogScooters. Will you be able to show(tell)me how to hook this up after we have our current issues fixed ? Or recommend the one you feel I need?
I did get a manual on CD, but it is for a Yamaha Vino 50 YJ50 2001-2005. I can mail it to you if you think it will help. Engine #'s NF1E40QMB and 990904383 stamped on housing above rear axle.

Ok I have been really busy, I have almost everything working, horn, turn signals, brake light,Fuel gauge and the starter works also. I still don't have head light or tail light.I have been tring to find a wire that puts out voltage when key is turned on to hook my head and tail light to, hope thats the right thing to do. While testing wires I found a 2 pin connector, it has a blue/yellow wire and a green wire, I only have a test light , but when I checked it with the key on it had low voltage, my test light lit up very dim, not bright like when touched to a battery. even tho the wire colors dont match, could this be my auto choke connector? The plugs do match.There is another two pin connector that has a green wire and a yellow wire that I have no idea where it goes, but would also hook to auto choke plug if thats where it goes There is also one red/white wire coming from harness that I am also lost about.So now I need to figure out how to hook up the CDI and coil and get some fire.The CDI has a 2 wire connector red/blk and grn/yell they are plugged in.From the CDI, red/blk goes to blk/red and grn/yell goes to white/grn from engine wires.From the engine the wires are: white/red female bullet connector unhooked,a 3 wire connector with a blk wire a yell/red wire and a white wire, the plug is unhooked. For a total of 6 wires coming from the engine.From the CDI wires are : red/blk and grn/yell with 2 wire connector which is hooked to engine, then a red/white wire with male bullet connector unhooked,a blk/white wire with female bullet connector unhooked,an orange wire with female bullet connector unhooked ,and a blk wire with male bullet connector unhooked, for a total of 6 wires coming from the CDI. The coil has 2 wires blk ground and a blk/yell wire both unhooked.I have no idea where to hook the blk/yellow. I cannot read a wiring schematic and don't have a clue what I'm looking at, guess Im a hook this wire there and that one over there sort of guy lol.Well crap, went to take some pics and the battery is exhausted on my camera, will post some later.