Hey, if you look a few thread down, you'll see us lamenting the lack of activity on this forum. Post away.

: Earth's Inner Colonies were bypassed considering Earth was
: found by accident, what happened to them?

Destroyed, as of Halo 3.
LOFTUS! FRONT AND CENTER!
Did, or did not, the journey to the Ark take several months?

If so, then there was plenty of time for Loyalist factions to continue their assault on Humanity. If the Cole Protocol was breached during the attack on Earth, this would only have made the Covenant's job easier.

: Brutes living alongside
: humans.... Jackals, ok that's sensible, not abominable gorillas)

Why not?

: As for the state of the Covenant, I'm really not all that surprised and don't
: see to much wrong with, if you look over the fact that the Arbiter somehow
: lost all the prestige he had with the surviving elites.

With what? And do you mean "Look over" or "overlook"?

: To start off there
: is the destruction of High Charity, which was just about quite literally
: itself infected by the Flood, and eventually completely obliterated. On
: top of that there's the Great Schism having its main brawl fought between
: High Charity's now divided fleet with both sides being pretty much
: decimated, especially since the Flood took part in the fight. Lastly the
: savior Master Chief himself along with Blue team taking out the Unyielding
: Hierophant and the massive fleet standing by around it prior to the
: formerly stated events. I'd say that has to account for a large majority
: of any authority and military might the Covenant held.

Like I said, I'm not sure that it did. The fact that High Charity had a fleet that size for an escort hints that the Covenant weren't hurting for ships, even after the destruction of the Unyeilding Heirophant.

And if you are correct, it's a retcon from the original intent of the Covenant's size.

: Regarding the 'Covenant Empire', much territory may have been conquered by
: the Covenant and therefore considered within their domain, but I always
: regarded the Covenant as existing more in the manner of flotillas. Each
: race still existing on their planet of origin, Sangheili I can see having
: a few colony worlds, other than that I viewed the Covenant as populating
: mainly ships, space stations in the manner of relay points and supply
: depots, and any planet-side infrastructure being for industry(mines,
: factories etc) and worker housing. This is just how I see it though, if
: canon exists that describes the Covenant Empire or just disproves what I
: said, then back to square one I guess.

I don't think that the above sounds very reasonable.
It kind of presumes that the whole of the Covenant empire is nomadic, and the only proof of that is High Charity (Built around a Forerunner spaceship and an asteroid) and the supply/harvesting we've seen that fuels the Covenant war machine, which has to be nomadic because the Covenant are fighting so far from home. There's also been the Jackal pirates, who hid in asteroid fields because that's the easiest place to hide.

So far, all evidence in favor of a nomadic Covenant has been pretty circumstantial. And why let perfectly habitable planets lie fallow?