Precision Shooting magazine sells (or at least used to) a book titled 'Precision Shooting at 1000 yds'. Not so much a 'how to' book as a collection of articles on long range shooting in various venues from varmint hunting to benchrest to an article on F-Class (that I blame with getting me hooked).
Bryan Litz's book Applied Ballistics for Long Range Shooters covers almost exactly what you're asking about - how to effectively utilize your sights (including scopes), how to set up and use your ballistic program for maximum accuracy, & some very good information on the effects of wind drift.
If you are looking for a book just on how to 'dope' the wind (different from theoretical discussion of wind effect) you might be interested in 'The Wind Book for Rifle Shooters' from Paladin Press. It is oriented almost entirely towards competitive target shooters on KD ranges with wind flags, but I think it still has some value in terms of general wind strategies, interpreting the conditions based on other (natural) indicators (because wind flags are all habitual liars...), etc. Basically if you can't figure out how to deal with the wind on a KD range with wind flags and such, your odds of success in the field are significantly reduced, IMO.
