Sounds like the identical problem to what Tom's is suffering with, which reminds me I was supposed to be looking up the wiring diagrams.
Markf:
How was the wiring when you removed it? Were the terminals onto the alternator corroded on the ends of the connectors?
Markf & Tom:
Lower the rear seat, and open then shut the boot. Does the boot light turn off?
Are the interior lights coming on for no reason when the doors are closed or the car is locked??
Also, check that the connections to the alternator, starter and battery are secure. Remove the negative battery lead, then with some sand paper, remove each lead, and sand the connector on each lead, AND the fitting, then replace and tighten up. On the right suspension turret there is a black cover, with brown wires going into it... Remove this cover, and sand the connectors and pins, then re-connect them again. Re-connect the negative lead.
Then check tension on the longest run of the drivebelt, by twisting it sideways. It should twist til the side of the belt is facing you, but no more. Whats the condition like? Really rough and worn, with cracks on the outer face means its time to replace it. Are you getting any squeeling from the drivebelt at any point? When was it changed?
I think the problem is likely to be an earth lead not earthing properly. I will try and find the time to look at the wiring diagrams in the next day or two and see if I can locate exactly where the wires are. A damaged wire wouldnt earth though, so I think its bad contact on either the alternator, or the starter.
Its by no means guaranteed to stop your problems, but its a very good start that isolates a number of possibilities.