Heh, awesome idea. I tried doing this a while ago, but my modding skillz are... minimal.
Suggestions:
-Hasekura Tsunenaga as the colonist leader for Japan. In the 1630's he traveled to Rome via Mexico City. (King is Shougun Tokugawa Ieyasu, or just 'Shougun of Japan'. And yes, it is shougun - it's a long o.)
-The Asians deserve firearms. In fact, before sakoku (the isolationist policy), Japan had the best guns in the world.
-Most of the Asians (excluding the Indians) should probably have Buddhism instead of Confucianism. Buddhism was a lot more widespread, and works better like the Europeans' Christianity, so you can have Buddhist Temples instead of Churches. (And it's actually a religion at all.)
-If you want an Arabian or Muslim nation, go with the Ottomans.
-Most of the Asians (excluding any Arabs) get a plus to diplomacy with Native Americans, since they're not there to convert anybody. (Maybe give the hypothetical Europeans a minus whenever they build a mission.)
-Elephants as a resource for Indians and Southeast Asians
-I like the idea of Vijaynagara
-I think it'd be more interesting if you went with the actual names of the countries (like Ming (for the dynasty) or Zhōngguó instead of China, Nihon/Nippon instead of Japan, Hanguk instead of Korea), but it might get confusing.
-If you want, start it at 1421 or somewhere, even though Gavin Menzies is an idiot. (He cites Washington Irving as evidence that Columbus thought he was in China...)
Civ suggestions:
-Overall
--Peasants instead of Indentured Servants, but maybe keep 'Free Colonist'
-China (Ming, or whatever)
--Treasure Ship replaces Galleon
---1 extra move, 1 extra transport capacity (or just call the galleon 'treasure ship')
--Maybe the Zhuge Nu (Chu Ko Nu is a mistranscription) for the non-veteran colonial soldier, normal musketman for veteran.
--Chinese Noble is a good idea instead of Elder Statesman, maybe Confucianist Scholar
-Japan
--You've gotta have samurai, it's just hard to fit them. Maybe it's just an extra unit choice, in addition to Ashigaru Musketeer and some form of cavalry.
---Here's an idea - you have three military profession choices: musketman, melee infantry, and cavalry. The melee infantry choice creates Samurai from Veteran Soldiers, and Ashigaru Pikemen from regular colonists. You could even replace the 'Veteran Soldier' with 'Veteran Noble' or 'Noble Soldier' or something, or even have both.
-Korea
--Hwacha replaces Cannon
--Turtle Ship replaces Ship of the Line
-Mongols (if they're there)
--Bonus to Seasoned Scouts
--Bonus to Ranchers (or whatever you call them)
--Keshik replaces Dragoon or Dragoon equivalent
-Khmer or Vietnam or whatever's in Southeast Asia
--Jungle defense and movement bonuses
(I don't know much about Korea or anything south of China, so that's all I've got.)
I think it would be fun to have the option to play with Asians and Europeans together, if not as a main game feature. (Maybe add a bunch more Europeans too.)