forgive the questions, I've not thoroughly read this thread. But a few ideas:
How is the engine behaving, and unusual symptoms?
Measure the battery voltage with a multimeter (cheap from Machine-mart), with the engine off, and then with the engine running. Blip the throttle, and see if there is a slight increase in Vs.
Check that the battery to engine and battery to body earths are all good. Believe one connects directly under the battery tray, and one near the PAS pump (This is on the V6, but can't see it being that different)
On the 2.0, there are three brown 0v connections coming out of the loom, in the injector rail area, near the front of the engine. Check these are all good, and trace them back for consistency.
Pop off the cable tray at the front, looking for any split/damaged wires.
There are three round connectors by the battery tray, they twist off. They are (from memory) white, blue and black? (stand to be corrected). Take each one off (bit fiddly sometimes) and re-seat it. Then pull back the rubber bit above each one to expose the wires - you're looking again for damage. Then look at the bottom part of the connector, are the wires all ok?
If you can get access to a Tech2 or something that can reset the fault codes, that would be wise - then you will only see the present codes. (leaving battery off won't clear them, because they're stored in non volatile memory.)
Post up after that little lot, and let us know how it goes.