Well it is with mixed emotion that I post this fix I'm sure you will see why if you read on.
Having ruled out every possibility for the starting issue (which interestingly enough had now become a hot no start rather than a cold hard start since the pump change)
Thinking over the systems and possibilities it all pointed toward fuel. We had drained fuel out of the system early on into a bottle, capped it (health and safety) and left it to visually check for any sediment or filings of which there were none.
How ever it suddenly dawned on us that no one had actually smelt it! Cap off and one whiff...PETROL!! AHHHH!!!
Such a simple test forgotten!
I have seen many diesels running incorrect fuel but this is the first time I let myself get caught out so I will treat it as a training exercise on not forgetting the bloody basics!
Drained out, refilled, test driven, perfect.
Seeing as how the fault changed I suspect the pump was In fact damaged by the fuel originally as was the injector (hot no start possibly caused by petrol vaporising?) The customer wants to drive it for now following our advice relating to manufacturer recommendations to replace everything.

Thanks for the replies, I hope this post alerts someone else in the future as to the importance of basic checks.

"Can't see the wood for the trees"