Just reread this and realized you say the PATS light is on was it on when it broke down? If this is the case then the key is not paired with the car, if you have swapped ECU and keys then there is no problem, (or you can just remove the transponder from one key and fit to another).
If you look at my post history there was a guy the other day with a RS2000 who had same problem, I said it was his key, he then got his key sorted out and it now runs!
In your case I would revert to the original ECU this should sort the immobiliser issue, the other things are probably separate simple issues.
Martin