I am nor an experienced modder, so my answers are not certain . But here goes:

Removing a faction: I think you have to keep the faction entry in the descr_strat file. Just remove all their settlements. On turn 1, the game engine detects the faction has no settlements and declares it dead. So you get an announcement of faction eliminated. At least, this is the way it was done in Unified Rome mod

World Wonder effects: The bonuses of the wonders (landmarks) are hard-coded. I tried to play with them myself. You can definitely move the landmarks, even have 2 of the same type (but only one will give the permanent bonus). You cannot have 2 wonders in the same province. All this is based on my own testing.

Effect of phalanx: can't help you on that one

Difference between named character and general: I think in the descr_strat file, named characters are really generals, and generals are really captains.

Spreadsheet question: The txt files were generated from a spreadsheet that the developers/designers at CA have . We (players and modders) do not have that spreadsheet, and we have to edit them directly. However, there are some nice editors out there (look for Hadrian and Caligula in the tools subforum).

Hope that helped.