Originally from Tech's 'Making a ToT Scenario' Guide on SL
2.0 Before you start
The Rules Txt. file in ToT is funny. Some things can be changed at any time just by editing the Rules file. Others can't be changed after the game is started for the first time, although there is often a workaround involving a special events file. So it's better to plan ahead and create a modified Rules Txt. before starting the game. Here's my list of things that are difficult or impossible to change once the game has been launched for the first time:
1. Maps: Rivers (difficult), other terrain (tedious)
2. @LEADERS: supplementary leader titles, eg. 'Archbishop' (impossible)
3. @CIVILIZE2: which techs can be owned and researched by which civs
4. @LEADERS2: same as above.
5. @UNITS_ADVANCED: Fields B, (impossible) D, E, F, (difficult)
6. @MAP_TRANSPORT_RELATIONSHIPS: (difficult)
7. @INITIAL_SETTINGS: (tedious)
Don't worry unduly about these right now. They will all be covered below. And, as mentioned, there are workarounds.