This subject is dear to me, since I too am in the midst of a Mod. So hopefully I won't get carried away and can contribute some useful ideas.
You have two basic groups you are dealing with, Mexican (Aztec, Mayan) and Peruvian (Inca). The first thing you have to decide on is if you are doing a historical or a non-historical mod, since the two different groups historically never met. And if it is historical, how to handle the European invaders. My personal preference
is non-historical circumstances but with historically modelled civilizations. I am not sure if you are also going to deal with native american civ's, which are much harder to obtain info on.
I'm going to give you two websites which deal with the different troop types that were available and should provide more than enough info on the unit types you should use.
Aztec
http://www.umiacs.umd.edu/~kuijt/dba105/dba105.html
Inca
http://fanaticus.org/DBA/armies/IV81.html
There are also references in the above regarding the enemies of each, which should provide you with some ideas on other civ's you may want to include.
Don't forget the scale. CivIII is a strategic system... each tile is 100 square miles. So while you have lots of missile armed troops, I don't feel that any of them should have ZOC or any missile ranges beyond 0.
Don't forget that the specialist troops were limited in size... Aztec Eagle and Jaguar warriors, the four (4) Incan regular units, European invaders, were relatively small numbers. Your Civ's should be building the majority troop type, not those specialist. Best way so far seems to be to limit the numbers by giving them those units initially and not allowing them to be built.
Mesoamerican civ's would generally speaking be considered a stone or bronze age civ... so don't forget they should not have horses or iron available to them. Baggage was generally hauled on land by porters and llamas (if Inca). While river traffic used boats, that is not modelled within the Civ III gaming system, so I would not worry about that aspect of it.... hmmm.. starting to get carried away, so let me refocus.
Techs... look at the existing Mod's and read their threads. Lot's of ideas on additional ancient techs. Don't forget to look at some of the Civ II Mod's, as there are some very good ideas there. Pick and choose the one's you feel are appropriate for your mod. Even so, you will probably end up adding or removing more based on your interpertation of whatever your source material is.
Worker actions .... I think a big decision you will have to make is how to handle roads. IMHO, roads in Civ III represent the type of roads that the Romans built. Since the Mesoamerican civ's did not have draft animals, hence no need for wheels, no wagons, etc, you could make a good argument that workers should not be allowed to build roads. I would also not allow mining and would restrict irrigation to the govt types that had bureaucrats (Theocracy and Centralized Monarchy, see below).
Governments... I mention this because I think it is a very important item in giving a Mod the proper "flavor". I would suggest the following: Autocracy, Tribal, Feudalism, Theocracy and Centralized Monarchy. Those should cover just about all of the govt types that the Mesoamericans had.
Hopefully, this will help. I'm looking forward to your units, as I would like to include them in my Mod, with your permission.
. I'm really glad someone has started to make a mod like this. Please continue with this mod as i do look forward to downloading the finished product.
