Edit Component Properties (Like the size of how much a lazer uses up in mass)
ShipComponentDefs.XML; a few special components are in SpecialShipComponentDefs.XML.
The Tonage of a ship (so i can create more space)
ShipHullStatDefs.XML for the base value of the hull class, the various *TechDefs.XML files for the bonuses available through the tech tree, RaceTraitDefs.XML for the empire bonus, IdeologicalGalacticEventDefs.XML for the bonus from the Design Revolution event, possibly some other files that I'm forgetting.
Speed Properties
ShipComponentDefs.XML for the bonuses from hyperdrive and thruster components, ShipHullStatDefs.XML for the base strategic speed and the base tactical speed modifier, GalCiv3GlobalDefs.XML for the base tactical speed.
You may also be interested in RaceTraitDefs.XML for the empire speed bonus available in faction creation (these are also used by the base-game factions, if I'm not mistaken).
Weapon properties (ranges, damage, etc)
Component attack scores, accuracy modifiers, range modifiers, and attack score modifiers are in ShipComponentDefs.XML; base fire intervals, accuracy, and ranges are in GalCiv3GlobalDefs.XML. Look in StarbaseModuleDefs.XML for the bonuses from starbase modules; remember that upgrading starbase modules replaces the old module's bonus with the new module's bonus rather than providing a cumulative bonus.
Some graphical properties (propagation rate or projectile speed, emission length or projectile size) are defined in FXBeamWeapons.XML, FXKineticWeapons.XML, and FXMissileWeapons.XML.