As mentioned earlier, all but about 3 of the original Nimrods were purpose built as Nimrods; ie they were not converted Comets. The 3 conversions (XV148 series) were involved in the initial proving trials and never saw front line service.
I worked on the initial stages of the project to choose a successor to the MR2 (in the PE). One of the bids was for refurbished P3s of the "lightweight" variety. Without giving too much away, there were concerns about how the aircraft had been treated in their service life (there was no complete "service history"), and the maintenance costs later in the aircrafts' life would probably have proved prohibitive.
The only parts of the Nimrod MR2 that will be retained for the MRA4 is the pressure hull, and that has been examined in great detail. Effectively they will be new aircraft (like my grandmother's broom that she had kept for 50 years - even though it had had 6 new heads and 5 new handles). The other reason for using existing structure is that the level of requalification is greatly reduced and I understand that it reduces the need to comply with some modern Defstans and other rules.
As for the R1s, I believe there is a plan to interleave refurbishment of these aircraft with the rest of the MRA4 program. The MRA4 production contract has not yet been signed, although it is imminent, so the R1 program is probably still in the discussion stage.
Shadwell