You'll have to go back and recreate a custom palette or open it using Load Palette in the Color Preferences. Gradients and patterns cannot be saved in the Preferences. You can save these in any document, though. All you then need to do is open that document and those custom patterns and gradients will be ready to use. You should strip any graphics from these files to save space.
Gradients are the schemes used in transitions from one color to another.
The first setting is for scrollback. This controls how many screens or lines you'll be able to scroll back to read. This is nice because text usually arrives faster than you can read it. If your memory allows it, set it to unlimited. Save screen before clearing will store the old data in memory rather than discarding it for those services that issue a clear screen command after each screen of data.