why are we now not nearly as comfortable (largely) with heights?

Well, the seeming universal fear of heights is definitely justified. Since the emergence of the genus Homo (2 MILLION years ago) we have been completely terrestrial. The australopithecines all likely exhibited a mixed behavioural repertoire that included a mixture of terrestrial and arboreal living (but most likely lived terrestrially for most of the day before finding a safe place to sleep in the trees at night). I guess the main point is that even for the australopithecines the trees were just a better option than dealing with vicious African predators at night (sort of "pick your poison" - heights or predators - at least with heights you are in more control of the danger).

Has enough time elapsed, in evolutionary terms, to have eradicated our affinity for heights

In terms of hominins (all species back to the common ancestor with chimpanzees) I doubt many of them had an affinity for heights. I should suspect that as soon as we start to see habitual bipedalism most hominins opted for a terrestrial over an arboreal niche when the opportunity presented itself.

many people do crave climbing etc, can this be attributed to our evolutionary past?

Tough to say, I've never read anything about that. It's entirely possible. I know chimpanzees and bonobos are both very good climbers and seem to enjoy it immensely.

Are there other examples of our now dormant past behaviors that express themselves on a smaller level than they once did?

Lots of tough questions! Any intense proclivities we have related to sex, sleep, eating, and socializing are all remnants of our evolutionary past. In regards to sex the deep desire to mate guard, or with food our strong affinity for sweet things, with sleeping our particular circadian rhythm tied to the solar cycle, or with socializing our ability to build and maintain large networks. Also physical things like being great long distance runners when compared to almost every other species - that particular trait seems to have evolved about 2 million years ago.