There are a few modifications that can be made to the Toyota FJ Cruiser drive line. The existing system has few weak links and seems to hold up well to off-road use. There are options to improve the gearing that include both gear replacement as well as additions to or replacement transfer cases.
If you have chosen to run over sized tires on your FJ Cruiser you need to consider re-gearing. This is especially true if running a manual tranny. The torque converter in the automatic provides some room to accommodate the larger tire sizes.