A friend of mine and I still fish the area around Buffalo Ford once or more each summer, although I think you could count the number of sizeable cutthroat on one hand that have resided in that stretch for the past several years (okay, maybe two hands). This summer I only made it there once with him, and although we did see several rising fish during the course of the day, this was the first year in the recent past that neither of us caught a single fish.
Although the numbers of larger fish have declined dramatically, due not only to the factors that you've mentioned but also to a number of consequetive drought years (that probably ended 2-3 years ago), what I have noticed for the past couple years is that there are more small cutthroat in this section now and that gives me hope that things might improve some in the years ahead. I agree completely that the Lake Trout probably came directly fom the Park Service stockings, although they'll never admit it, and I saw pictures of an almost 30 year old Lake Trout caught in Yellowstone Lake, taken about 10 years ago, so they've most surely been there for many years (although not in so large numbers).
Also, in the section of the Yellowstone that I fish extensively (north of the Park) I've noticed many more Cutthroat in the 5-7" range this year than I've seen in a number of recent past years. So, while the picture could always be better for the future, I'm pretty optimistic that things are on the upswing.
John
p.s. The first issue of Fly Fisherman Magazine was in 1969 I believe.