Hi Jim,
I spent a while testing tonight and found a few things, but haven't managed to fix it yet.
All fuses in both fuse boxes check out OK, so unfortunately it's not something simple like that.
I don't think it's power or grounds to the engine ECU either, despite the seeming lack of communication with the immobiliser - I've checked those at the ECU socket and they seem solid - also I replaced the two ground terminals on the engine block (M4A and M4B) not long after buying the car, so a problem there is unlikely. The grounding of the engine to the body also seems fine. (Anyway if it wasn't, the starter would struggle, and it doesn't)
I thought about trying to query the engine ECU with the Lexia but I remembered that you cannot talk to the engine ECU at all until it has been unlocked by the immobiliser keypad, (it won't even respond) so no use checking that! I also remembered that my Lexia has never been able to talk to the immobiliser keypad, (possibly due to the wiring of the 30 pin adaptor cable) so I don't think I'm going to get any help from the Lexia...
What I have noticed is that the central locking, clock
and radio are all not working. The alarm seems to be partially working because when I reconnect the battery the blinkers flash twice, however the alarm doesn't go off as it normally would after removing the battery.
At one point in my fiddling the car sprang into life - I think it was after I slammed the bonnet shut. I noticed that the alarm activated as if the battery had just been reconnected (blinkers flashing constantly - no horn because my alarm horn has never worked) and the immobiliser showed just the red light instead of red and green and the clock had started working - I tried keying in the code and starting the engine and it started and ran perfectly while the alarm continued to flash the blinkers...
Realising that the only way to reset the alarm was to lock and unlock the doors with the fob I switched the engine off and pressed the lock button - there was no sound of door locks activating, and as soon as I pressed the lock button the clock which had previously started working faded out again. Sure enough, I was unable to start the engine again and the immobiliser was back to both lights on.
So despite the immobiliser communication problem it seems like the root cause of the problem may be the power or ground supplies to the central locking system - and apparently the radio and clock share either power or a common ground point with the central locking. And somehow this is indirectly affecting the immobiliser. (There is a connection between the central locking drivers door switch and immobiliser)
Another thing I've noticed is the red LED on the dashboard that is part of the alarm (?) that normally comes on solid with the key and flashes with the key off is not coming on with the key and then a while after the key is turned off it starts flashing very faintly also suggesting a power problem to the alarm as well...
I think to fix this problem I need to find out where the supply and earth connections for the central locking come from, and whether they are shared with the radio, clock and immobiliser...
So is there any chance of the wiring diagrams for the radio, clock, and the central locking ? I need to find out the physical location of any shared earth returns and/or shared power feeds...
Edit: you already posted the central locking and alarm circuit diagrams and I can see there are a number of earth points shared between them, but you didn't post the diagrams that show the physical location of the earths, which I would need to actually find where they are.
