I too have a '99 750, and I get by with the Haines Manual (which only claims relevance up to '96) and the 2000 parts diagrams (which you can download as a pdf doc from the ducati.com site).
Between them they have let me work _most_ stuff out... I've discovered a few things that aren't quite like either the Haines stuff or the '00 parts diagram (I wish they'd put up the '99 pdfs too!):
Main case gasket - the Haines manual carefully explains how to allow for the thickness of the gasket when calculating shim sizes to preload the main bearings. Ducati stopped using gaskets there sometime after '96 - they now just seal the cases with goop (threebond was what I ended up using)
Starter sprag clutch - the one that came out of my bike isn't quite like either the one in the Haines pictures _or_ the one in the '00 parts diagrams, and its also not the same as the one my local dealer got in for me. Fortunately, and bit of swapping around of parts between the old and new sprag seems to have made one that both fits and works (I have ended up with a "spare" circlip, but its got 10,000km on it now, so I'm pretty sure I got it right)
Alternator - the alternator is different on my bike to the Haines pictures. This caused some confusion on reassembly (but I cant remember twhat was confusing about it right now)
Clutch - my '99 seems to have a clutch in it that no-ones ever seen before... Its not like the pic in ether the Haines Manual or the parts diagrams :-( The "standard" replacement over here is a Sureflex 1815, but that doesn't even come close to fitting in mine - its ends up being about 5mm too short and the pressure plate just doesn't move that far in. Its also slightly differently configured in that I've got 8 1.5mm steel plates and 9 3.5 aluminium friction plates for a total thickness of 43.5mm. I _think_ I'm going to have a new clutch in this weekend using a set of plates that Mike at Gowanlochs has a pile of - they're 2.5mm steel friction plates, but with 1 extra of those and another steel plate I'll have the right thickness (with 12% more friction material area too!)
Having said that, I think you'll need to be doing some pretty serious tinkering before you run into serious problem that you won't be able to sort out using Haines and the parts diagrams...