@Xiggy, thanks!! Your theory is freakin' awesome! Especially because it includes all games in the series and uses the info about DQ X.
Here I'll also try to present my theory about timeline, though it has some dissimilarity with yours. This timeline is rather simplified, it includes for the most part game of the main series.
Firstly, I'm not sure if there are two "twin" timelines (simultaneous?) since DQ III had Zenith castle as bonus dungeon as well as Zenith Dragon in that castle. Probably the alternate timeline is correct only for XI? I prefer to regard all game information as canon, it's easier.
Thus, including two DQM games which synopses I read, here is as follows:
11->DQM->6->3->1->4->8->10?->5->2-> Caravan Heart-> 7->9.
The most difficult part is to establish the sequence between 4, 8 and other games. As we see Torneko character in 8th part and know about Ramia's past, we can place this part after 3. Part 5 is clearly in the future (probably, far) of the 4, so it is even more distant than 8.
Then, in DQ 7 (its prequel is Caravan Hearts) we see one of the bosses, Estark, which is a progeny of the original Estark form fourth and fifth parts. In addition, manga gives us info that the world of DQ 7 is in fact very distant future of the DQ 3 (transformed after the First War??). The ninth part has no clear relations with other parts, though it has Observatory which can be the same as Zenithia or its legacy. Also, it has the bosses from all previous parts. Here we find the end of the God's story.
@JaybirdC, in fact I thought rather of the kalpic cycle, not of post-apocalypse world.