seeing as its got a new chain, cassette and cranks, it definitely sounds like the freehub imo
replacement springs and pawls are in order i'd say, if you're wanting to keep the hub, if not you can usually pick up wheels/hubs on here pretty cheap
EDIT: what hub is it?
The Hub is LX, which I bought from a seller here (on Mavic 221)
shimano are notorious for the free hubs going, if i remember rightly they only use a 2 pawl system
my xt recently started letting go too.
The bike has just been finished and ridden now, this is how the seller described the wheels;
The hub is LX M563 on Mavic 221 rims.
I bought the wheels from trek_y back in November last year (2012)
This is the sale thread;
This is how the wheels have been described;
Wheels - Deore LX M563 black hubs, Mavic 221UB rims, DT spokes - hubs nice and smooth, no dings or wobbles, come with Shimano classic chrome skewers. £55. Or £65 with Specialised Nimbus 1.5 semi slicks, tubes and 8 speed cassette as shown.
All I did was change the cassette to a 9 speed one and put new set of Continental's on.
And they do sound nice! But as you said, freehub.
I'll see what i can do, (as listed above re. chainline, chain length BB size) if no luck, i will change the freehub