Sorry to hijack this thread, my VL's doing a similar thing at the mo. It's been converted to manual (before I bought it). Just over a month ago I started de-looming the engine bay, first up i hid all the headlight wires behind the guards, when I had done that I hooked up the battery and they worked fine.
Because it's no longer manual, I chopped all the plugs off that used to be for the Auto Trans, (NOTE I did keep the thicker purple wire - the one that goes from the ignition switch down to the starter motor). Hooked up the battery again and everything started fine.
Then I started the process of moving the battery to the boot, chopped all the leads coming off the positive side of the battery and re-routed them to run behind the brake booster and down the firewall then out to the engine (starter motor + alternator).
Then ran an 8Gauge cable from the starter to the alternator, then a 4gauge cable from the alternator to power the rest of the car's electrics.
At that stage I hadn't moved the battery yet, so (I am 90% sure! - it was a few weeks ago now) I hooked it back up to make sure the car started and it was fine.
Then I put the battery in the boot, ran a 35mm sq cable from it directly to the starter motor. Another 35mm cable from battery negative down the the floor of my boot (sanded a big spot back to bare metal).
So finally that was all done, I hooked up the battery, fuel pumps primed, starter motor turned over as normal, but the car wouldn't fire up, I tried it 5 or so times but it sputtered once or twice and that was it, kept cranking but wouldn't fire.
So I pulled out #1 spark plug (lead still on), held it against an earth point, got my brother to turn the key and nothing happened. absolutely nothing (i think the fuel pumps primed but that was it), starter motor solenoid didnt click or anything. didnt turn over, nothing.
Then I did a diagnostic on the ecu, from what I gathered, it said there was a fault with the Throttle Valve Switch or something. Had a look in my workshop manual at the wiring diagrams, it seems as if that switch is connected to the Auto Trans Ecu, (my Auto Trans Ecu is still in the car).
But that's as far as I got, I wouldn't have a clue what to do from here, any ideas?