Hope you don't mind I answered what I could.
-How did the Toa acquire noble masks? Were they given or did they find them?
I'm not positive but I'm pretty sure they found them like they found the Great masks. Hopefully someone else can back me up or correct me on this.
-When did they get the Makoki Stones?
Again, not certain about this one, but I'm pretty sure the Turaga gave them to the Toa when it was time to enter Mangaia. Unless they sent them on a scavenger hunt for them, too, but I don't remember reading about that.
-Is there any canon explanation that Greg can come up with (even on the spot) for the use of the words Tohunga and Koronan, the descent into the Suva to get the golden mask, the Mana Ko in the Mangaia in Legend of Mata Nui (video game)?
Koronan would just mean 'villager', I guess, so I don't see any reason to consider it non-canon.
-How come the 2001 storyline is so messed up from all the different sources (MNOG, Tale of the Toa, LoMN video game, Comics)?
Cathy Hapka wrote the books then, and Greg wasn't involved in MNOG, so that would explain some of it.
-Why was there a floating golden Hau in Onu-Koro?
Greg might not know this, because he wasn't involved in MNOG.
-How come Ka is a Kahu in MNOG but a regular Gukko in MoL?
Again, Greg wasn't involved in MNOG. But are you sure the Gukko in MoL was meant to be the same bird?