Can you activate an ability during the end step after the 'at end of turn' triggers have already been put on the stack?

The end step is a regular phase step that follows normal priority rules. When the end step begins, any triggers with 'at the beginning of the end step' are placed on the stack, then players receive priority in turn order (CR 500.2, 503.1). At this point — and at every subsequent point when the stack is empty and priority is passed — any player may activate abilities or cast instants.

Priority works in a loop: after a spell or ability resolves, the active player gets priority again. Even after all 'at end of turn' triggers have resolved, players can still activate abilities as long as they have priority and are within the end step (CR 116.3, 116.4). The step only ends when all players pass priority with an empty stack.

There is no rule that locks players out of activating abilities once end-step triggers have been put on the stack or have resolved. The end step behaves like any other step in this regard — it just also happens to be a common window for 'cleanup'-style triggers.

Concrete example: Your opponent's Scavenging Ooze has an 'at the beginning of the end step' trigger that goes on the stack. In response, before it resolves, you activate your Mystical Dispute's flash ability — wait, wrong example. Better: the Ooze trigger resolves. The stack is now empty during the end step. You now activate your Vault of the Archangel, tapping it to give your creatures lifelink and deathtouch — this is perfectly legal, as you still have priority during the end step.

Citations: CR 116.3 covers when players may activate abilities; CR 500.2 covers the beginning of a step and placing triggered abilities on the stack; CR 503.1 specifically covers the end step beginning.