Much is made of the mainplanes being different sizes. This was entirely normal given the production processes of the day. Every aircraft I’ve ever worked on had the problem to a greater or lesser extent. What matters is how you control it (in the sense the differences between tail numbers and serial numbers must be known and recorded). How do you do that? By implementing the airworthiness regulations.
If you don’t, and it is a simple fact that it was policy from 1988-on not to implement them in order to save money (actually, to generate funding to offset deliberate waste elsewhere), then you lose control. Even if you think you have control, the same regs require you have the corporate knowledge, experience and willingness to listen to and act upon engineering advice, so that when planning the programme you make allowances for Risk Reduction (and ill-fitting mainplanes was a known risk, and notified to senior management many times).
In the same MoD(PE) Directorate General, at precisely the same time, another major conversion programme had exactly the same problems, albeit on a smaller scale, only this time caused by differences in production runs. Question – Why is that aircraft in service and not languishing in a hangar? Because the regulations were implemented, despite orders not to from the 2 Star in charge of both programmes (and also Chinook HC Mk3).
As has been said above, given the sheer scale and scope of this known risk, your basic problem was the procurement strategy. I’m sure there were valid reasons for modifying MR2 (despite the rule of thumb, never mod a mod). I can’t really think of any, but someone will know. But, the decision was made and the way ahead was clear; and ignored. To call the programme Nimrod 2000 was a howler. As I said before, there was at least one (that I know of) technical and contractual pre-requisite whose ISD was late 2001, so Nimrod simply couldn’t be delivered before then. Apart from MRA4 “delays”, the main effect is on the legacy MR2 project and its funding. There is what is called the “5 Year Rule”. As the ISD was announced as 2000, MR2 funding would reduce gradually in the preceding years, as they could not demonstrate 5 years useful life of, for example, modifications. Other areas such as tech pubs would run down (even further than dictated by the 1991 policy). Instead of buying economic quantities of spares, only small, short term, expensive buys would be made. (Recognise all this from the QinetiQ report?). And every time a “delay” was announced, MR2 would have to make a compensatory bid to restart the 5 year clock. The dangers are obvious; compounded by an unwillingness in PE to notify such “delays”, leaving MR2 high and dry. (One 3 year slip was continually denied). How many times did they restart the 5 year clock? How many across both programmes know WTF I’m talking about? That’s Corporate Knowledge, Experience and all the other fundamental airworthiness principles I talk of. Also known as Common Sense.