There are a few fundamentals that must be understood before tackling this failure.
1. It is systemic. Refusal to recognise this results in the immediate problem, in the aircraft under discussion, being resolved, but the same problem in others being ignored. The Nimrod Review accepted this (he didn't actually reveal anything new) and recommended an MAA, not a Nimrod authority. With Nimrod now scrapped, hey presto, most of the problem is gone. No need to do much else. Let's *** off early, it's Monday afternoon. Until the next imminent grounding or fatality.
2. Airworthiness and serviceability are two different things. The former facilitates the latter. There is no need to work backwards through the problem. What MoD won't acknowledge is that this is well known. It was the subject of numerous scathing reports in the late 80s and 90s, and formed the basis of the main evidence to the Nimrod and Mull of Kintyre Reviews.
3. Attaining and maintaining airworthiness are different from Fitness for Purpose. With all due respect to Service engineers at front line (and I've done 1st, 2nd and 3rd maintenance, and managed 4th), they seldom see the first two. If they do, the system has already failed, big time. Their focus is on FFP; as is the MAA's, only they don't realise it. They think they're addressing airworthiness but six years on haven't started. I'm sorry if that upsets them, but the proof is in the pudding. Moreover, it was predicted here on pprune before they were even stood up; and confirmed almost immediately when it became known who was conducting their initial audits (as mentioned by Engines). This is why you get people on here denigrating those who attain and maintain - "It's all bollocks, let's just get on and fly". The reason why they never saw or even heard of this before was because it was done quietly and efficiently in the background, as a core subject by properly trained people. This is not a 2 year tour job, it is a long term vocation. MoD personnel policy militates against this.
Normally, one would revert to known good practice. There is very little evidence of this in MoD today. It is actually formal policy not to employ people who would provide it. It is therefore ludicrous to expect MoD to resolve this in a reasonable time without serious help. Worse, one cannot expect more than a mere handful to recognise the warning signs and see it coming; so help is sought far too late. That, despite the Nimrod and MoK Reviews pointing the way; not to mention a raft of Inspectorate of Flight Safety and Internal Audit reports from the 90s. Significantly, hubris plays a major part.
A few years ago, the Chief of Defence Materiel, Bernard Gray, submitted a report to the Labour Government that got perilously close to suggesting going back to mandated policy. He was then appointed by the Tory/Lib Dem Coalition to implement it. He called "his" initiative "GOCO", Government Owned, Contractor Operated. The trouble was, none of his lackeys had told him it was 95% mandated policy, and that a detailed submission had been made to one of his predecessors in January 2000 suggesting the same thing. (No reply). As soon as this was put to MoD, by a Lib Dem Minister, they promptly denied Gray had even mentioned it. Hubris again. But, it is actually a good idea. No one is left in MoD to do this work, so get a decent industrial partner to help.
An effort was made to implement GOCO. Word is, it failed (in its original form) because (a) MoD could not articulate the requirement, and hence (b) Industry could not cost it. (I'd add a third - no competent company bid, probably because they saw that MoD hadn't a clue, so trouble loomed). Where does it tell you how to articulate and how to cost? (And even how to control the data required to do it). The cancelled Def Stan I mentioned before. All roads lead it. It is THE Bible. Again, hubris, because MoD don't want to admit the solution is staring them in the face, but they have instructed staff not to implement it.