0)You sound kind of new, so I figure it's probably a good idea to link to the
Modding Guide on the wiki as well as a list of all the pages with the various
tokens that you use. You might also want to check out the
Raw Explorer Utility which can help you put things in the right places and not make stupid mistakes.
1)New limbs and stuff affect the creature, so all the changes that you will be making will be in the creature files. (So if you wanted to make a human with wings for example, then you can copy paste the human raws into a new creature, add the 2WINGS token to their body, and then set the entity to use your new creature.)
2)This is at the bottom of the entity in the position tokens. A good example to look at is the dwarven entity, where if you scroll down far enough you will find [POSITION:XXXX] tokens. The [NAME_MALE:X] and [NAME_FEMALE:X] tokens then control the names of the various positions IIRC.
3)You can't. You can change what type of city they settle in (so mountain halls, forest retreats, actual cities, dark towers, etc.) but you can't change the symbol.
4)PANTHEON makes the civilization have a pantheon of gods associated with different things, similar to dwarves and humans. REGIONAL_FORCE makes the civilization worship the "spirits" of nearby rivers and forests. Having no RELIGION:X tokens means that they will always be ruled by demons similar to goblins.
5)Language files can be edited just like anything else, and are present in the language_xxxx.txt files and then the civilization chooses which language it uses with the [TRANSLATION:XXXX] token. They are
extremely tedious to edit without an outside automator such as
DFLang though.