Davejb,
Re your points...
I've raised it a number of times, but there can be a time factor involved in airworthiness (ALARP) assessments. I don't know whether this applies to Nimrod, or any of the QQ recs, but its important to recognise that it could, and furthermore it is not unusual to do so in civil or military airworthiness circles.
The link below takes you to a mandatory civil airworthiness directive. It stems from the TWA800 accident in 1996, and this particular one (there will be lots of others) requires some mandatory changes to A330 & A340 aircraft to reduce the risk of fuel tank explosions, for instance by changing some of the clips used on wiring harnesses etc. This one came into force in 2007, but the A330/A340 aircraft involved must only comply by 2009. They do not need to be grounded in the meantime.
http://ad.easa.europa.eu/ad/2007-0278 *
I think your point 3 is valid - MoD could probably benefit from clarifying the situation and avoiding this speculation.
You can probably see from the above that your point 5 is not necessarily black and white. Note that you wouldn't expect the QinetiQ report to comment on timescales for embodiment - they probably wouldn't have had the complete picture to advise on this, though they could have been consulted since then - this is probably likely.
* I should add that if you have a fear of flying I wouldn't recommend browsing all the ADs on this site. As crimewatch used to say, "don't have nightmares".