Thought I'd throw this up for anybody on teh internetz searching - for anybody looking to install a spy 5000m (or similar) alarm/immobilizer by themselves, here's a few notes you may find useful.
The spy 5000 (at least) requires an extra 12v relay to work with yamaha bikes (for remote start function only - everything else works fine without this extra relay). You can pick these relays up in the local auto shop for like €4.
Anyway the wire that activates the remote start (turns on the starter motor) - the blue wire on the spy 5000 alarm - goes into the "85" leg on the relay.
Legs 86 and 87 are joined together an to an earth point. If it is a five leg relay then leg 87a is just left alone.
Leg 30 is joined to either the Blue&white (live) wire which is the input to the starter button, or the Black wire that comes out of the Starting Circuit cut-off relay (the rear-most of the 2 little black boxes which sit under the tank at the front, just above the front cylinder head). This black wire from starting circuit cut-off relay is actually the same wire as the Blue&white one of the starter button, it just changes from one colour to the other at a terminal connector in between the cut-off relay and the start button.
Doing it this way means you only by-pass the start button itself, not the safety circuit i.e. clutch & neutral switches etc.
You don't actually have to cut into any of the bike's wires at all. You can piggy-back on the same connectors as the bike's wires join onto.
Finding space for the alarm brain unit, microwave detection unit, siren, antennae and LED is nigh impossible on a stock 1100.
If you remove the useless AIS, this opens up some space under the right panel. If you don't want the tool-pouch, you can remove that too for space. I have pod filters on mine so the stock airbox is gone and makes loads of space for the alarm brain unit.
You have to keep the brain flat so mine is cable tied to the horizontal balancing pipe that joins the 2 pod filters.
I put the microwave detector unit under the rider's seat.
The antennae can be cable-tied to one of the upper cradle bars under the tank, or put where the AIS used to be, or like mine - in the space between the rear cylinder head and the chassis.
The LED fits nicely in the plastic trim that goes around the ignition key barrel (just drill an 8 - 8.5mm hole in it).
The siren sits snugly on the back of the stock air filter case, right between the two cylinders (you have to cut off a small bit of useless plastic on the back of the air filter case to get it central).
If you have pod filters then the stock air filter case is empty and you can actually run the siren wire up through it and the stock air duct to the alarm, so it's completely hidden.
The alarm's main earth wire can be bolted to the chassis using the same bolt that used to hold down the rear of the airbox (that is, if you've removed the airbox to put on pod filters).
This is also a great point to secure the extra relay.
If you're looking for the two indicator wires that the alarm hooks into in order to flash them - these are the green and dark brown wires that run to the tail of the bike.
You can just plug in the wires to the same 5-wire white connector the green & brown wires connect to. It's under the plastic trim thing (under rider seat) that holds the ignition unit.
In order to hook up the immobilizer, you'll find the ignition fuse (15A) in the fuse box (yamaha have a nice little label guide inside the lid) which is located under the right side panel. Again you can just piggyback the relevant wires into the rear of the fusebox section where the ignition fuse goes.
Although yamaha's need an extra relay to turn the starter motor when you hit the remote start button on the fob, you also need a 100 ohm resistor to bypass the anti-hijack feature on the XVS 1100 ignition key barrel. If you take off the tank and the plastic trims around the ignition barrel etc you can reach the wires that come out of the back of the ignition barrel.
You bridge the Black&Blue wire across to the Blue&Yellow wire (on the ignition barrel side of the plug/unplug terminal connector), or the Black and Blue&Yellow wires at the far side of said connector.
What this does is permanently makes one of the 3 connections that turning the ignition key would make - because the remote start on its own can only make the other 2 of the 3 connections (for this model at least).
BEST TIP: carry the fob in a pocket where the remote KILL function button cannot be pressed by accident while flying down the road at 75mph