This is seriously cool, and I appreciate the work that went into it. Your discussions of class roles in Mystara, the race writeups, and the sections on the Immortals are just awesome. I really like the way you implemented some of the BD&D aspects (like Weapon Mastery). Though I'm not clear on why you feel there should be no dragon sorcerers or wild sorcerers. Sure, they didn't exist in Basic, but neither did Warlocks, and you found a way to integrate them.
The section on building costs is great (maybe not the most necessary stuff in the world, but a welcome addition), and integrating the Secret Crafts as a prestige class is pretty cool. I could go on.
A comment and suggestion: the Backgrounds section should have a heading indicating where the backgrounds start. It's easy enough to deduce, but having a heading title like the Class Options right before it would make it easier to read and less jarring.
All around, an amazing effort, and greatly useful even for non-Mystara campaigns.
That being said, this latest version adds a bunch of stuff I don't recognize. Where did "Fire Wizard" come from? "Gallowglass?" "Troubleshooter?" And many of the options you show as subclasses might work better as backgrounds. The Bounty Hunter, Gallowglass and Troubleshooters for example - these seem like concepts that would appeal to and draw members of more than one class. There would be no sense in making a "Homeless Person" or "Guy With A Job" subclass - these are roles and categories that many different people could fill or fall into.
Though I really like your writeups of them, I'm also hesitant to have the Matter, Entropy, etc. spheres be discrete cleric domains. Like the subclass options described above, doing so seriously restricts the number and type of characters that can be affiliated with these ideas. That wasn't the case even back in the days of "let's arbitrarily restrict everything we can" Basic D&D. It certainly doesn't seem to fit with the broader 5e ideology.
EDIT: I just noticed that the "Mixed Blood" background appears twice, on pages 68 and 70.
Also (and I'm sure that this is something you were planning to adjust one you had the final art and the general layout is finalized), the page numbers in your table of contents are no longer accurate.
There is a typo in the Extra Attunement feat; it closes with "You may attune an additional three magic times" (which I assume was intended to be ". . . three magic items." Which also seems way too powerful to me, incidentally, especially since it can be taken multiple times. One additional item per feat would make more sense to me).
You also have fairly frequent punctuation issues (commas where colons or semicolons would be more appropriate, stuff like that). I don't know how concerned you are about it, though.
)
