The only thing I think I removed was the top intercooler hose. There is mention in the WSM about undoing the exhaust pipe joint between the downpipe and mid sections but I just left it in place and it was fine, there's enough flex in the exhaust system to allow it to move enough.. I used a piece of wood to support the turbo assemly and another piece as a lever to lift it back into place.
The nuts were seized onto the studs that came out of the block. I just treated them as bolts when putting them back in though I should really have removed the seized nuts and reseated the studs - the exhaust manifold studs are only torqued to 10 Nm whereas the nuts are 45 Nm. I've got some new studs for when the manifold comes back off and will use the nut and locknut method when I do fit them. If you can maybe get some spare studs before you do the job.
I would suggest using paraffin to clean out the inlet manifold and also intercooler if it hasn't been done yet. Make sure theres none left in though before starting the engine. My 300Tdi Defender has never had EGR fitted (it was an MOD whitefleet vehicle) so my manifold was cleaner than I was expecting for 150k miles.
Colin