Well, it's finally all back together! Thank you all for your help and encouragement. I've just been out and done 20 miles and it all feels fine. The various whines, whirrs and vibrations have gone, so I can now moan about wind noise instead! I've left the undertray off and I'll check for leaks / top up as necessary tomorrow.
Lessons learned, if it might help anyone in the future:
1. On a TD4, FL1, there's no point in taking the exhaust off.
2. Taking the IRD pinion housing off before removal helps lighten it a bit and gives you a bit more space.
3. I was lucky because someone has replaced the right hand bottom balljoint at some point and it is bolted through the wishbone, so I was just able to take the bolts out and that let me slide it out far enough to get the right hand driveshaft out of the IRD.
4. slackening the subframe bolts and leaving it hanging on them, gives you a bit more space to get the IRD out.
5. Go for an IRD rebuild kit with a cooler. It really is easy to break them while trying to take them out!
6. IRD bearing kits seem to come with an element of luck! There are shims in the IRD which, I'm sure, ought to be added to or subtracted from, to get the right clearances. I ended up swapping one from the big bearing on the driveshaft end of the IRD to the big bearing on the crownwheel side, and it was only luck that gave me the correct clearance! It seemed to have become necessary because instead of sending two Timken bearings, (which is what the box had in it when I opened it up), they'd sent one Timken and one Koyo. They were the right size, but I think the Koyo was thinner than the Timken.
7. Make sure you get all the seals too (and ideally, the O rings). Mine came with no o-rings so I've reused them and am trusting to luck!
8. Getting the old bearings out of the IRD is the hardest part of the job. An impact gun for the big nut on the crownwheel is your friend. Some of the outer races for the bearings (in particular, the one inside the big diff gear) are very hard to remove. You can't get a puller of any description under the edge of them, or poke them out from the other side. I ended up using a die grinder to carefully grind the inner race away until I'd weakened it enough to relax its grip on the housing.
9. A bearing splitter / separator is a worthwhile investment for some of the other bearings.
10 As Nodge said, it was one of the big bearings behind the crownwheel that had failed. The others (whilst there was some wear evident), didn't look too bad.
I didn't bother stripping the pinion assembly. The bearing in it felt fine and it's another one that needs to be shimmed - plus there's a collapsible spacer in there and you can't get replacements now.