Cut-out relay location - cautiously optimistic it's cured!

[unfazed]

Your original loom will be colour coded so re-joining them should be pretty simple,

This is  the odd thing - the immobiliser is under the seat. Near it, and part of the loom, is a 6 wire connector plug. One side of which is all red/white wires, the other is all black wires. The red side (female) has a purpose made connector plugged in that connects all the pins and is capped with a plastic cap.


The male side of the connector has had  five wires cut and joined to the plain black wires from the immobiliser. Looking at the Haynes wiring diagram the connector looks like it was intended for an alarm system.


There is a relay in the immobiliser, so hopefully I can work out what gets connected when the relay switches on as it seems to isolate the start button / relay at the least.

What type of alarm is it?
Post a picture of the plugs you are referring to under the seat and I may be able to help you identify what you need to do.
There are plugs there for pluging in an alarm and are usually bypassed.
Have you checked the wires to the alternator (Generator) as the pick up  for the ignition is in there and can be damaged by removal and replacing the alternator cover. Often overlooked when checking for electricial problems.