bear in mind, when I say timetable, I don't mean it has to be directly tied to the passage of time.
More that if the PCs "waste" too much time, events happen such that the remaining encounters change.
Thus, it's OK if the party took longer on a given fight, you're not measuring minutes. But if the party stops for an extra day, or basically spends significant time doing things that aren't intended toward the quest, then the bad guys move forward in their plan.
I'd also not take a literal "one quest at a time" approach, barring the party ignore/drop a quest. It's possible the party may try to multi-task/solve some quests. That's up to them, and if they juggle fairly well, I'd let them do it.
What I'd recommend is that for any significant encounter (say BBEG), plan for 3 states. The first is what/where is the bad guy if the party pretty much heads for him, without siginificant delay. For drama, you can make it seem like the party arrived just in time, or possibly before the villain is fully ready.
The second, is for what if the party dilly dallies too much (resting when they should be traveling, ignoring the quest more than they should). For this state, the party should feel lucky to arrive just in time to stop a nefarious plot. His finger may be hovering over the launch button. Security is already prepared for the party's arrival, making it harder to get into the complex.
The third, is for if the party is "too late", basically they pretty much ignore the quest. The last state means the villain has already succeeded, pushed the button, the missile has not only launched, it's detonated, and the goal is achieved. The party hears about his victory (unless they were in the blast radius).
As a GM, you have to eyeball what state to put things in. Generally, the default state is where everything's like a typical adventure. You go room to room, scene to scene. You don't advance the time state, unless the party blatantly wastes time. It's OK if they choose the wrong direction (and head back, in fact, a good DM leaves a clue after the first mile that they went the wrong way so the party FEELS like they're behind). Imagine this state to be like the typical random dungeon. Monsters are wandering about, doing their day to day stuff. Award full XP for finishing the mission.
The "alert" state happens because the party doesn't get engaged with the mission. Stopping to rest for a day or more inside the dungeon is a good example. Other denizens of the dungeon will find the dead bodies of their dungeon-mates, and put the facility on alert. It's probably large patrols will form, and ultimately surround the room the PCs are holed up in. Award XP for the original mission, not extra for any added encounter difficulty.
the "too late" state, is for last resort. The players have totally disregarded the situation. The bad guys win. The game world is changed because the players didn't seriously try to save the day. Award 0-half XP for the original adventure.
Note: I advocate adding up all the XP for encounters, assuming the "default" state. Give out this amount or less, based on party success/time wasting.