I'm glad you like my ideas Amra I'm always happy to give them. I'm still struggling to tackle your biggest obstacle which is your second UB and UU problem.
I know abit about Native American cultures, particularly Mesoamericans, so I'll try tackling that first:
Toltecs:
Second UU: Atlantes Warrior: Replaces Swordsman for the Toltecs, has one extra point of strength but costs five hammers more.
Second UB: Great Temple: Replaces Universitys for the Toltecs. In addition to the knowledge boast also gives a culture boast as well. Costs more hammers however.
Iroquois:
Second UU: Forest Prowler: Musketman replacement for the Iroquois starts with the forest attack and guerrilla promotions. (Remember always that Bernie made a ton of Iroquois units)
Second UB: Siege Workshop: Replaces the Alchemist, gives Siege Units bonus expierience when trained in the city that builds one. (The Iroquois were experts at using European gunpowder weapons. This building would be a special longhouse where such weapons would be reverse-engineered and constructed.)
Sioux:
Second UU: Rifle Rider: The Sioux managed to defeat the American army many times with their cavalry tactics. Especially when they managed to get their hands on guns. This unit replaces the Heavy Horseman and comes with an extra chance of withdrawing from battle(hit and run tactics).
Secondary UB: Chief's Teepee: Where the stories of the past were handed down, diplomacy with other tribes was conducted, and other such things. This building would replace courthouses, add a knowledge boast in addition to the lowering of maintenance costs, and come earlier in the tech tree, perhaps at Oral Tradition?
Mayans:
Secondary UU: Ah-Kuy: The Axe was a sacred weapon to the Mayans, and in mayan society only the elite of the elite could wield it. Replaces axeman, has a greater strength against other melee units than other axeman type units and one plus strength, but five plus hammer cost.
Graphic:
http://forums.civfanatics.com/downloads.php?do=file&id=6094
Second UB: Mayan Observatory/Temple of the Stars: The Mayans were called the stargazers. One of the biggest things they are known for is their observations of the heavens. This building would replace the observatory, and give a small culture boast in addition to the science(and cost a slight bit more) and also come earlier, perhaps with the Calender.
Heres a graphic you can use:
http://forums.civfanatics.com/downloads.php?do=file&id=8712
The Aztecs:
Secondary UU: Eagle(since the first unique unit is called a jaguar why not eh?): Replaces spearman, has an even better attack against mounted units than other spearmen.
Secondary UB: Noble's Temple: Replaces the castle for the Aztecs, also units trained in the city gain a free promotion, just like as if it were a barracks in the city. Comes earlier in the tech tree as well, with Masonry.
Possible graphic:
http://forums.civfanatics.com/downloads.php?do=file&id=8748
The Navaho:
2nd UU: Medicine Man: Replaces the scout for the Navaho, can also scout but also has the medic promotion. Loses anti-animal bonus however.
2nd UB: ???? Wish I could be of more help here. Seems you got them covered. Maybe a House of Weaving or something?
Non-native Americans:
Thai:
2nd: UU: Nak Rhomp: Replaces the Pikeman for the Siamese. Has a small bonus against melee units as well as the normal anti-mounted bonus. Costs five hammers more.
Khmer:
2nd UB: Wat: Replaces Theater. Wats were temples that the Khmer built around their cities. These would provide even more culture than theaters but would cost more hammers. Maybe less with stone...