[RPG] Portent and spell preparation: which comes first

The halfling's Lucky trait deals with the die roll (PHB, p. 28):

When you roll a 1 on an attack roll, ability check, or saving throw, you can reroll the die and must use the new roll.

And so does Advantage/Disadvantage, since it refers to the same trait (PHB, p. 173):

For example, if a halfling has advantage on an ability check and rolls a 1 and a 13, the halfling could use the Lucky trait to reroll the 1.

The Divination wizard's Portent feature, on the other hand, deals with the check as a whole:

You can replace any attack roll, saving throw, or ability check ... with one of these foretelling rolls.

And here comes the interesting part - the three emphasized terms are only mentioned in rules as actions, not numbers:

• The description of attack rolls (PHB, p. 194):

  To make an attack roll, roll a d20 and add the appropriate modifiers. If the total of the roll plus modifiers equals or exceeds the target’s Armor Class (AC), the attack hits.

• Saving throws (PHB, p. 179):

  To make a saving throw, roll a d20 and add the appropriate ability modifier. [...]

  A saving throw can be modified by a situational bonus or penalty [...]

  [...] proficiency in a saving throw lets a character add his or her proficiency bonus to saving throws made using a particular ability score. [...]

• And ability checks (PHB, p. 171):

  To make an ability check, roll a d20 and add the relevant ability modifier. As with other d20 rolls, apply bonuses and penalties, and compare the total to the DC.

All three go the standard way:

1. Roll a d20, get a number
2. In case of (dis-)advantage: roll another d20, get a new number (or keep the old)
3. Add bonuses/penalties, get the final number
4. Compare the final number with the AC/DC and get the final success/failure answer

From the strict RAW reading of Portent, we have to replace steps 1–4 (the whole check) with a number (foretelling roll), which makes no sense, as the result has to be boolean – success/failure.

If we loosen the restrictions, the logical thing to say would be "In the context of Portent, attack roll/saving throw/ability check is the number to be compared with the AC/DC" (i.e. the result of Step 3 above). In this interpretation "You must choose to do so before the roll" means that the decision is made before Step 1 and therefore no actual die roll happens. The modifiers are applied to the foretold roll as normal. This interpretation is reinforced by an unofficial tweet from March 2015 by rules designer Jeremy Crawford:

The portent die is intended to replace a d20 roll only, not any modifiers applied to it.

This result is Rules As Intended as well; the whole point is that the character knows in advance what is going to happen.

No, spells must be prepared when you finish a log rest.

The section on Preparing and Casting Spells for the wizard states:

you can change your list of prepared spells when you finish a long rest.

If it said something like "anytime after you finish a long rest" then sure. But as it's worded you can only change your list of prepared spells when you finish a long rest. Failure to do so leaves you with the same set of spells you had prepared the day before, not open slots to fill later.

This is also backed up by Jeremy Crawford, lead rules designer in this twitter exchange:

Lebedev Dmitry
^@LebMit
@JeremyECrawford Can spellcasters prepare spells not all at once, but leave some "slots" for preparing spells later during the day?

Jeremy Crawford
^{‎@JeremyECrawford}
You prepare your list of spells only at the end of a long rest.