havok91,
You did not really specify what this gearbox will be used for. The end use requirements will make a huge difference in how you design and analyze the gearbox, and also in what reference material you use in your work.
If it's a racing gearbox with limited life requirements, low weight requirements, no need for high production rates and little concern with cost, then you will design the gearbox in one manner. I don't know of any good texts covering race gearbox design. Your best bet would be to get friendly with someone that works at a company like Xtrac, Weissman, Hewland or Quaife, and pick their brains.
If it's an on-road gearbox, needing quiet operation, smooth shifting, long life, high reliability and low cost, then you would design the gearbox another way. The hardest gearbox to design, by far, is the production automotive gearbox. Designing gears, bearings, shafts and synchro rings that are durable, low cost, easy to assemble and totally reliable is incredibly difficult. The best resource for production automotive gearbox texts is the SAE. But they're not cheap.
Good luck.