A final update on this from my side., and some embarrassment as well
. I finally have the car up and running sweet as can be. It goes for its MOT in a fortnights time and then to be sold (to fund my other car). So, just in case someone is doing this and isn't mechanically minded (like me), I'll let you know where I went wrong (big time).
First up, many many thanks to all those who put forward suggestions and procedures for doing this. I have to admit cutting corners on one major part though. As part of fitting the pump onto the toothed belt, I used ElsaWin and turned the engine over until OT was visible through the oil filler in the engine. My (very wrong) assumption was that the engine was now aligned properly, and proceeded to fit the pump, which resulted in the issues of difficult starting and continuous plumes of white smoke and running like a tractor.
I have to say that I suffer from depression, so since things don't go right, I leave it, and that was the way with the car. Every so often I would go and have another go at sorting it out, with the same result. Then for some reason, I decided that I would follow the ElsaWin instructions 'to the letter' and bought the locking kit of eBay. Remember, I'm not mechanically minded, and this sounded an even more difficult and awkward job to do. So, after the kit had been lying around for literally weeks, I set about fitting it.
This is when I discovered what had been going wrong. I aligned the engine initially to get the OT as before. When I then went to fit the locking plates, I noticed that the camshafts weren't aligned with the slots, and the locking pin wouldn't fit either. Using a cheap boroscope (off eBay) I finally managed to get the hole aligned, and fitted the pin. The locking plate just slipped into place. I then locked the pump and fitted it, and then put the battery on overnight charge.
Next morning, connected the battery (which was on its last legs) and also used jump leads from the other car. Got in and turned the key. The car started literally within a second. I got tons of white smoke out the back, but considering how much unburnt diesel had pumped through the exhaust over the previous months, that's to be expected. Connected up VCDS and let it do the timing. It has been running fine ever since, with the only additions being a new battery and some REDEX in the fuel tank.
Moral of the (long) story is follow the instructions to the letter, even if it does mean you have to learn something new. About the only place I went wrong was relying on the information given to me by the mechanic. If I had VCDS beforehand, I would have been able to pull the error codes when I first had the problem and the J399 wouldn't been there. That took me down the wrong route which cost me £250 for a dud pump, £150 for the mechanic to fit it and whatever it cost me to have the immobiliser disabled, none of which was necessary.
So, once again, a very big thank you to all those who contributed their knowledge. It wasn't wasted, it just took some time to sink in.