Well Guys, I replaced the entire lock and window mechenism on n/s rear door and it cured the problem, Interior light now going off when shut and the alarm has now starting working again without any issues.
Even the lazy locking works now.
The wires in the loom had been butchered, looks like that at least 4 wires had been cut and botched
:doh:
I soldered the wires, but the interior light wasn't working when opening door, obviously with all the botch up in there it was just shorting out everywhere so the replacement was the easiest option.
Thanks for all your help,
If you every need someone to strip your car, I've become a dab hand at it now