Fall of Reach, First Strike, and Halo Reach are all canon. Now, a lot has changed in the canon since Fall of Reach was released (when Brutes, Elites, and Hunters were first encountered for example), but the core of the story is still true. Now, the Fall of Reach is told primarily from the point of view of the Master Chief. As such, he is unaware of the Covenant invasion force on Reach in July and August (until August 30, of course). Halo Reach, on the other hand, if told entirely from the point of view of Noble 6, who has a very different experience and never meets the Chief or any Spartan-IIs (Jorge not withstanding).
The reason people have a problem is because they cannot see how the two stories can take place in the same timeframe. I’ve addressed that issue here.
> I have heard that the novel has actually been revised since the game came out, in order to make the two consistent. So you may only encounter discrepancies if you read an older version of the novel (printed before 2010).
The books are mostly the same. The reprints address issues such as when Elites, Brutes, and Hunters were first encountered, but overall, the books are the same. However, the reprints contain extra stories at the end.
> 2. The Spartan III’s - In the game, everyone on Noble team is a S-III except for Jorge, however they all have Mjolnir. In Ghosts of Onyx it says the S-III’s were only given SPI armor, not the better Mjolnir. I don’t know if there is another source that could explain this but I haven’t found anything on it yet. In addition, every Spartan in Noble team has shields on their armor by late July, but in the book John only gets his upgraded Mjolnir with shields on August 29th - one day before jumping from Reach to Halo. Again I have not seen an explanation for this.
The existence of Noble Team and them wearing Mjolnir is addressed here.
As for shielding: Mjolnir mk. V was first issued in November of 2551. Data from these early suits was used to make the final suits used by the majority of Spartan-IIs. The armor the Chief’s received also featured something Noble’s did not: the ability to carry an AI such as Cortana.