Okay, a update on this little saga

Popped round to the masters abode last night for a bit of investigation with his Tech2 contraption

It would seem that even though the initial reprogramming of all manual settings was installed on the cars engine ecu a couple of weeks ago, because the gearbox ecu was left connected by myself the engine ecu could still see this and because said gearbox ecu didn't have a gearbox to play with anymore, it decided to spit its dummy out and throw codes at me

Also when it was disconnected, it got futher upset and that's why I ended up with the TC light on too
Okay, a bit more info on the cruise setup .........
After we looked at the wiring diagrams on TIS, it would seem that the V6 manual facelift cars with cruise DO have a clutch switch and this is supplied with 12 volts from a ignition live fuse / circuit, through the clutch switch and back to a pin on plug X36 on the main ecu

Even though its all reprogramed and all warning lights have gone, the revs still hang on a little but nowhere as bad as before. Whether the clutch switch has a effect on the revs hanging on a little when playing I not sure but we will see in the near future when i've sorted out the new wiring ect.
More details to follow later on pin identification ect and i'll take a few pickys to add to the guides when its all up and working.
If i've got any of that lot wrong, i'm sure somebody will be along soon to smack my legs

As always, thanks to Mark and all others who have helped (including Serek who did the spanner work in the first place)