He was referring to when he was asked his opinion of if firing the Halos was the only solution to stop the flood. Why he mentions this to the Master Chief as if it was the Chief himself who asked is/was interesting at the time (CE days, or Pre Halo 3) as it didn't make much sense to the fans.

In Silentium this conversation is revisited at the end of the book, where the (iso?) ((Good)) Didact directly asks 343 GS if it were up to him to pull the trigger (as it were), would he do it?

This comes full circle with Halo CE and, in my mind, alludes that Master Chief himself has an imprint of the Didact in him, or a Gaes of him, as how else would 343 GS bring up such a topic and conversation that ONLY the good Didact could know?

I think this will come full circle yet again in the next few games/novels and we'll learn that the Chief indeed is the spiritual incarnation of the Iso-Didact who is pitted yet again at the Ur-Didact (the one we see in Halo 4) .

: 2. Why did Regret jump the gun and send his ships to Earth before the rest of
: the Covenant.

I forget. Something to do with unearthing the Portal and wanting to get there first.

: 3. What did Truth dig up in the Legendary ending of ODST?

I can only assume it was the start of the Portal leading to the Ark.

: 4. What questions did the Gravemind ask Cortana, and what answers did she
: give?

You should re-read the short story in Halo Evolutions that covers this. It's pretty good, despite that it is written by Traviss.

: 5. If blowing up Halo is enough to stop the flood from spreading, why did the
: Forerunner not just blow up all the Halos? Yay, flood gone!

If they blew up the Halos to eliminate the flood within the proximity of that explosions (such as installation 04 and 05) that would not have affected any of the flood beyond that explosion.

Simply put, the Halos still needed to pulse. They still needed to actually fire to take out everything in that radius.

The only analogy I can think of is you are surrounded by bad guys, but rather than fire your pistol and take out as many of them from a distance as you can, you opt to just throw the damn thing really hard at the guy in front of you to kill him. Sure, you might hit him in the temple and drop his ass, but there are still dudes behind him that now you can't do anything about.

: 6. Why does the Covenant hate humanity again?

I'm assuming you mean post Halo 3?

Simple.

The "Covenant" as you are thinking of it no longer exists. You have remnants of those factions who are starting anew. Some will go there own ways and rebuild. Others will still harbor grudges, some still will believe in the original promise of the Covenant.

The largest faction you have are the Elites who view Humanity as a plague on the galaxy. A force not unlike the Flood, who will expand and consume and destroy others simply to advance their own race.

These Elites want to stomp Humanity out not because they are an affront to some religious sect, but because they feel their very existence as a species is threatened.

What's worse, is they are right. ONI is trying to murder all the Elites they can by any means they can: Political infighting, proxy wars, to more sinister and highly unethical means such as sterilization and poisoning of their crops and livestock.

So the Elites are trying to unite whatever they can muster to fight Humanity. Some use the facts mentioned above, some (such as the Elite Protagonist in Spartan Ops) use false religion (exactly as the prophets once did) to blind others to their cause.

Jackals have no loyalty beyond profit. They are mercenaries. They fight with whoever bids higher for their services. They have no main loyalty. This is why there are Jackals fighting with the Elites AND with the Insurrectionists.

Grunts are still slaves. They have no choice who they fight and what they fight for.

Brutes, Drones, Most of the Hunter majority: It has yet to be seen or explained where their factions are headed or how they are doing.

: Many thanks.

Hopefully that helps.