I have recently changed the engine in my cbr600 f1 for a lower mileage one.

The previous owner seems to have botched the connector together from the alternator.

Would anyone be able to tell me which colours go to which yellow on the connector? I have included a few pictures for help. Any help much appreciated!

Connector from alternator

Back side of connector

Current botched solution from previous owner

 

the 3 yellow wires should feed directly to your regulator rectifier, i am unsure which wires it was feeding into, could you share some more pictures of where the wires lead too?

 

Hi, as you can see (bottom right corner) from this beautifully colored diagram shamelessly stolen from CorruptFile the three yellow wires from the alternator go to the regulator.
The two green wires are either spiced inside the harness or on the connector and go to a ground eyelet.
The two red wires are also spliced together and go to the starter relay main fuse.
I highly recommend to clean all power connectors from rust and gunk, they may cause an increase in resistance which is turned into heat that ends melting your connectors.
That's most likely the culprit of the botched wiring, or he installed an aftermarket regulator with the wrong connector.
The three yellow wires don't have a specific polarity, the regulator takes the 3 phases from the stator and rectifies them one at a time through a series of diodes.
the rectifier doesn't care which phase is generating a charge, if it has ac on one yellow wire it rectifies it to dc on the red wire. (caution this is true only for this type of easy and rock solid stator-rectifier configuration, some bikes use one or more coils to generate the spark pulse that goes to the CDI, and on newer models who knows what type of software trickery goes on in the regulator)