If whirlpool prevents a runner from jacking out do they have to access the upgrades (say, edge of the world) do they have to access it at the end?

I guess the question is: does completing a run require the runner to access all possible things (cards behind remote server, hq, rnd, upgrades etc)

They have to access. If you look at the timing chart, step 5 is after passing all ICE. The runner must choose to continue or jack out. Whirlpool (if it fires) prohibits jacking out, so the runner has no choice.

The runner has no choice, they must access all cards in the server (if a remote).

However if the runner has something like Bank Job they can choose not to access and take the cash instead (or whatever the card allows) or runs into an ETR ice and choose not to break it (they aren't jacking out, the ICE forced them to end the run).