well...........good bike to start with, parts readily available from breakers, and new from yamaha. You didn't say whether it is a UK bike or grey import, but it makes little difference where parts are concerned.
I have just completed a very similar job, (see 'number four makes her entrance') we (my son and I) have spent a couple of months and about 600 quid (on top of the purchace price (£300) to end up with a bike that is essentially as good as new.
and to be perfectly honest, we could have done it for half the price, but as the engine was in bits (and as Beeman says) you tend to see all the worn bits ( which don't really need replacing) so a rebore, new piston and new oil pump, gasket set, new tappets etc etc is £200 up the pipe straight off!
so get it roadworthy and mot'd, then see about prettying it up later
and good luck
you'll find plenty of advice/help/ pi55taking here
SteveL