[jambo]

OK,

First phone the alarm company and ask if misisng the LED would affect it in this way, if so, solder on a new LED (They are directional, so you may need to find a way of telling which way to go, or try it both ways)

Failing that:
Your imobiliser will probably have 2-3 pairs of wires going into the loom. They will probably be black to stop people with no time being able to bypass them. For each pair you will find they go into the loom at a seperate point. There will be an original wire cut, and each end will be attatched to one pair of black wires. This means that instead of the wire just being connected as normal it now has to go through the imobiliser and will only work when the imobiliser closes a switch and re-connects this wire.

1st check these connections into the loom are good and tight and a connection hasn't come adrift.

If you bridge each pair in tun and try to get the bike to start you can see if it's just one pair or all of them. Either way connecting each of the pairs together means you bypass the impobiliser and the bike should run. This will confirm your problem is definatly the imobiliser.

Warning: Doing this involves some cutting of wires or preferably just scraping off some insulation for each of the lines, if you aren't careful you could end up making work for yourself or someone who might may charge you quite a bit for fixing it!