MacOS – Managing Grouped Terminals

Terminal.app has these colors hard-coded into it. Internal methods like +[NSColor(Terminal) vtRedColor] use hard-coded floating-point constants to set the colors.

As you noted, there are SIMBL plugins that can patch this but you've already noted their current limitations. SIMBL has been updated to support 64-bit applications, so you should contact the authors of the plugins to request that they rebuild them to support 64-bit. There's also another SIMBL plugin to consider.

The only other option for Terminal.app is to write a feature request at http://bugreport.apple.com and hope that somebody at Apple is enticed to add color customization to Terminal.app for Lion.

do you ever try Relaunch application:

Relaunch saves you time by taking Snapshots of which applications you are using, and starts them back up for you. Think of it as a launcher on steroids that lets you switch between work contexts with one click.

you can take a snapshot before restart your system and after that double click on the snapshot you created then it restored all your files and application you worked on.