A couple of things:
Re: Samurai Armor.. how bulky and encumbering it is depends
entirely on what time period you're looking at. Early 'samurai' armor was full lamellar scale armor, adopted from Mongolian armor (this would be around 500 AD). Later samurai armor (such as used in the Warring States period and in almost all popular samurai drama) had a very different purpose. It has the famous paneled look because it tried to deflect projectiles rather than anything in melee. Presumably if you were fighting in melee, it was a test of skill rather than metallurgy.
Thus, the primary factor in late period functional samurai armor was to leave the samurai mobile. Thus, it was incredibly light.
You could actually model this in Dominions with a low-prot armor that granted Air Shield.
As for the other Sinuyomijomon changes, very cool. KO, I volunteer my services for helping with fleshing them out. I note that almost all Buddhist elements in Jomon are esoteric. Are there any plans on importing the more popular Buddhist sects (like the Amida cult) into Dom3? I would think the Celebrant event could be modified quite well to show this, if nothing else.