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So you're saying I need a new field coil as well as a new regulator? Also Im a bit confused should I be looking for a field coil compatible regulator or rectifier?

You need the field coil regulator only! This is what your charging system is misssing!

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You need the field coil regulator only! This is what your charging system is misssing!

Scirocco if you read through the test results when the field coil was completely disconnected ( green and black) it was showing a full ground (12v between battery positive and green field coil wire) this is probably what caused the failure of the original regulator 

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So you're saying I need a new field coil as well as a new regulator? Also Im a bit confused should I be looking for a field coil compatible regulator or rectifier?

You need a regulator ( the rectifier is the diode pack that the three yellow wires go to - on your bike this is a separate unit) the tests you carried out (battery positive to green wire with black wire disconnected) showed 12v which indicates the field coil is shorted to ground which is probably what caused the original regulator to fail

Okay so off the relay that is supposed to be the regulator there are 5 wires connected into it. There's a green from the field coil, a black that ties into the common ground, a brown that is just tied in with a bunch of other browns. I assume off the wiring diagram and the manual that these are the proper 3 that are supposed to go to the regulator?

However, there is also a red coming straight off of the rectifier as well as a orange that is tied into a white with a red stripe. The white with red stripe come off of the starter solanoid and then goes into the fuse box.  They all look like stock wires, however, I am very confused as I see no white with red stripe on the wiring diagram even though it is specified in the inside writing of the fuse box. Also I see no orange other than a turn signal wire so this confuses me as to what that could be for. Ive attached some pictures below. 

Ill go ahead and swap the field coil from the spare engine in but I wanted to try and figure out some of this wiring first so then I can just plug everything in properly once im done. Thank you!

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Okay so off the relay that is supposed to be the regulator there are 5 wires connected into it. There's a green from the field coil, a black that ties into the common ground, a brown that is just tied in with a bunch of other browns. I assume off the wiring diagram and the manual that these are the proper 3 that are supposed to go to the regulator?

However, there is also a red coming straight off of the rectifier as well as a orange that is tied into a white with a red stripe. The white with red stripe come off of the starter solanoid and then goes into the fuse box.  They all look like stock wires, however, I am very confused as I see no white with red stripe on the wiring diagram even though it is specified in the inside writing of the fuse box. Also I see no orange other than a turn signal wire so this confuses me as to what that could be for. Ive attached some pictures below. 

Ill go ahead and swap the field coil from the spare engine in but I wanted to try and figure out some of this wiring first so then I can just plug everything in properly once im done. Thank you!

It is midnight now in the UK but I will look tomorrow. All that should go the regulator is the green field coil wire, a black ground and a brown ign live. The red to the rectifier should not be there. Some Kawasakis use white/red as the main supply from the battery to the main fuse ( it may not be the original fuse box)
If the red/white is on the battery side of the starter solenoid and is the only wire feeding the main 20amp fuse that is ok
The rectifier should have four wires, the three yellows from the armature (I believe these change colour at the plug) and one output from the rectifier to the battery (looks grey on the diagram but may be the red that you have) this should go to the battery, nowhere else as this is your charging wire.
There should be nothing tied into the red/white fuse supply as this would be unfused and a significant fire risk.
Whilst there may be some colour variations the number of wires and where they go should match the diagram exactly

Okay thanks I lot I really appreciate your help so far. I understand what your saying about the red wire being the grey thats what I was thinking but im not sure how it plugs in and to what exactly. Although im still pretty confused about the orange one. 

Okay I ordered a stock regulator off of ebay and it should be here in a couple days. Im going to swap in the other field coil. How could I test the feild coil and the outer part of the "stator"? as I might just swap in the whole other side cover to make it easier. Thank you.

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Okay thanks I lot I really appreciate your help so far. I understand what your saying about the red wire being the grey thats what I was thinking but im not sure how it plugs in and to what exactly. Although im still pretty confused about the orange one. 

If the red is the output from the rectifier it can either go to the battery positive terminal or the battery side of the starter solenoid (be careful how you route it as it's an unfused battery live. I see no purpose for the Orange and would remove it as it's a fire hazard.

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Okay I ordered a stock regulator off of ebay and it should be here in a couple days. Im going to swap in the other field coil. How could I test the feild coil and the outer part of the "stator"? as I might just swap in the whole other side cover to make it easier. Thank you.

For the field coil you can measure the resistance between the green and black (spec should be in the manual) and check between the green and the mounting point ( continuity) to check it doesn't have the same problem. Should read open circuit.
The stator you would check as a resitance measurement between pairs of yellow wires (again spec should be in the manual) and also check there is no short to ground between the yellows and the mounting point

Alright Ill disconnect the orange and just tape it up then. How exactly would you go about connecting the red thought? I think it would be kind of had to put it straight to the battery terminal but you said to be careful mounting it to the starter solanoid. Where would you mount it on there? Like right where the battery line connects to the solanoid? And Ill go do those tests on the stator and see if the one I got is good. 

Also the field coil in the bike now has no movement if it at all and is stuck down to the cover, however, the one in the other parts engine can move around and isnt stuck down. Which is the correct one? Should it have no movement in it? It doesn't seem like its got any bolts to hold it down though.