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I was thinking that is where they went to, so it appears that part of the harness is missing, they should continue back to the soloenoid and probably end up at the CDI for safety precautions, and probably your 2 relays are missing, i havent seen them in any of your photos or the CDI, is it there or also missing. They might have deleted them and wired it direct with the romex.

Good you had a drain, the one i was working on didnt have a crancase drain, and took forever to get it out with a syringe.

Drained the oil out of crankcase and it rolls over now. Just need to clean the carb and she if she fires up. I'll provide an update within the next week.

The 3-pin and 4-pin plugs go into what I thought was the main harness. But following them around, they all go directly to the START switch, engine stop, and mystery switch above those in the video below: The 3-pin goes to start/stop. The 4-pin goes to a black slide switch above those that is unlabelled. I'm sure any owner is going to know what that switch is for, and I'll watch that 1988 video @Gwbarm posted now.

Thank you guys for the input i will try removing the carburetor to verify it and get back Bob

That's the problem they just won't fit anymore I'm so lost as to what I'm doing wrong I've already lossened it all the way and it's the actual "hydraulic" height that's to high I'll grab some pictures tomorrow

It sounds like you adjusted them too much , the shocks are designed to be able to adjust on the bike by clicking up to the next step, they really need to be attached to be able to do that, not familiar with your bike , but they are usually fairly easy to adjust on the bike by turning it. You said when you put them on they fit but were out of adjustment, were they too high or too low. If you get them back to the way they were and reattach to the bike and see if you can adjust to the right height.

This videa may help a little with your wiring:

Rancher, you could use the continuity setting on a meter and test from one cut end, to the end of any other wires the same colour, anywhere on the loom. That would give a good idea about what the cut wire's meant to be for.

Im looking at the plugs trying to see what they may be for, can you tell what the other end hooks to , i couldnt tell from the photo

I'll grab one tomorrow that's what I was thinking it shouldn't affect the hight of the spring just the stiffness

Well if it went in the other day it should go in again.. I'm not familiar with that bike but most shocks you can adjust in place. Mostly when we adjust the spring tension of a shock it doesn't change the length of the shock. The shock is usually fully extended by the spring and adjusting the spring makes no difference to that unfitted length, it only adjusts how far the bike drops once the weight comes on it. If you lift the bike the shock should fit no matter how the spring's adjusted. Perhaps if you can post a photo of the setup on that bike I'll spot a problem.

There should be a short brass tube on the bottom of the carb for a rubber hose I'd think. The leak.. There's a drain screw on the bottom of the carb I think, and that might be leaking. Other than that it shouldn't leak unless the fuel level inside the carb is too high. I think you can check the fuel level before removing the carb. To adjust the fuel level, or fix the leaking float level valve, you will be best to remove the carb and clean it and check the rubber parts aren't worn or perished. You might be able to remove the bottom of the carb in place but it's best to take the carb right off, strip it entirely, clean and inspect it all and then reassemble it and it should be right for years.

I'm not familiar enough with yamahas to be much help here, but I would definitely say repair the old wiring rather than trying to jury rig some other model wiring in there. To figure what the cut wires are for I'd look at what's near by on the frame or engine, and then go check a or several wiring diagrams looking for those coloured wires being shown connected to one of those things I'd identified near the wires. I'd also keep referring back to partzilla to see what other model wiring diagrams I should be looking at. When I looked a few parts up it seemed that your bike shares parts with wolverine, moto4, BB and kodiak, and over a range of years.. To identify exactly what components you have on your bike is going to take a lot of familiarising yourself with the bike and looking through partzilla, and even then It might be tricky to know the exact details about electronic parts. The shape, colour and pin locations of plugs, and wire colours, are clues when looking at wiring diagrams and identifying parts.

It seems like the rear end of the bike won't drop down far enough

You mean the length seems wrong now ? Have you tried lifting or lowering the bike so the shock mounts line up ?

The only yamaha i have to show photos of is a Big Bear and its 10 years newer than yours but may show where the starting componets hook up. T The battery and soloenoid and relaus sit on top of the plastic on this one, yours will be different but around your battery tray there should be brackets or something similar to hold the components. Black coming from starter to soloenid, red to battery, Plug in with blue, blue /white and red going to start switch 2 black boxes are relays. The other is fan controller. Behind aall that is the air box which i didnt see on your photos, mine was missing also.

So I installed a new shock on my 125 yesterday sadly it wasn't adjusted right I took it off to adjust it tried to install it again today and it no longer fits I loosened the nuts on the spring again and it still won't fit idk what I'm doing wrong when I try to install it but I'm lost any tips or videos would be great thanks.

@GwbarmIf I can get a member who has a 1989-90, to tell me what goes into the 3-pin and the 4-pin connector, just under the left side of the tank, then I can fix up the rest well enough to do as you say, the engine etc. It feels and looks solid. Just janky electric is my guess at this point.

I think the first thing i would do is evaluate the engine and transmission, make sure the engine has good compression. Then jack up the rear wheels where you can turn them by hand and make sure it shifts though the gears correctly. Of course they can be fixed also but i like to start with engine and transmission then see if it will run.

The small hose may be a vent hose, but that would not cause a leak, if you carb is leaking its usually a stuck float needle float not working properly or gasket failure.

Hy there great to be able to communicate with people having knowledge I have a continuous problem with a leaking carburetor and I just saw a small rubber hose detached from the bottom of the carburetor and i cannot find were it should be attached and how the two side should be affixed to the carburetor any suggestions as i cannot find a description plan on it thank you Bob

Well it appears you have been busy. You definately have a project, thats a good thing if you like working on them. As far as the wiring harness goes yours looks fairly descent, you can professionally repair your existing harness easier than replacing it. What you have to do is study the wiring diagrams, very carefully to determine where the butchered wires go and what it connects to. The dangling down cable you were referring to goes into the carb, that is your choke cable. You may have somethings missing like the starter cutout relay i didnt see that which might have been cutout and wired together. You should have a plug next to the soloenoid that controls the power going to the starter, maybe. It looks like your air box is missing and the hoses that connect it to the carb. You can see diagrams of what all is missing by looking up your model on Babbits, or Partzilla. The white with red and white with green may go to your pickup coil im fairly familiar with Yamaha wiring, but havent worked on one that old in a while. The only problems you may encounter with your harness if you want to put it back to original is if plugs have been cut out or missing. Your in a good place a lot of us know these older bikes, look forward to helping you piece it back together. Where would you like to start. My advise would be , do not get overwhelmed, take it one piece at a time, one day at a time. It will eventually come together. I know iv been right where you are many times, a great learning expierience.

@Mech that is very helpful information! There is a post you probably have not seen yet, as it is awaiting approval. Here is a photo of the forward mystery wiring. This is just underneath the left side of the gas tank, extending down. Two wires were cut from the back of the 3-pin coming off the harness, and 'hot wired' -nutted- to the romex, with black going to one main terminal on the solenoid, and white going to the other. The same terminals had both the heavy red wire and heavy black wires connecting to them. Don't ask me what the prior was trying to do. Here's the notes about the wire color codes: I looked at both the 87 and 90 wiring diagrams, and neither have a 3 pin and 4 pin connector that correspond to these. That's why an actual pragmatic layout wiring diagram would be useful, to show actual people what goes where... oh but then insecure designers would be afraid of being less needed. I guess.. These colors are as accurate as I could determine. There may have been some color fading. Where I put multiple options, it was not clear. White 3-pin connector: Yellow w red stripe Black w green? Yellow? black Black 4-pin: Red Red w yellow stripe red w black stripe brown