my first thought was the bearing preload seems to have been lost.
were any locking collars or locknuts loose on the spindle?
does the sound get worse as he operates?
i'm assuming he's kept oil in the bearing reservoirs and the clunking is not caused by a lack of lubrication.
from what i have seen and read,you remove, spindle locknut and retainer, the chuck, and bearing retainer & set screws and spindle set screws the spindle comes out towards the bed.
i have read that a man made a custom puller that went through the spindle kinda like a reverse collet closer, that draws the spindle out from the headstock using allthread and some nuts and a couple fabricated collars.
i imagine you could be a little more cro-magnon and use soft materials (lead,brass,wood,aluminum, etc) to use as a drift to drive the spindle out (being careful not to damage spindle or threads of course).
i hope the information helps out!