I have a 300 tdi and just flushed the intercooler with brake clutch cleaner in situ with the pump sprayer from unipart seems to have worked a treat wouldnt say it was cleened out perfectly but well enough to notice a difference
Er to be honest i cant remember but id fitted the large intercooler without opening the cooling system.
Then when i was going to sell the car i removed the large cooler and fitted the std one.
From memory i think i removed the viscous fan and shroud then i think i dropped the cooler in from the top, but this was 3 or 4 years ago.
I bet if you ask any of the cooler makers they know the quick ways to fit them.