So I ended up going with these guys to change out my gears. Its been 3 weeks now, and so far so good! As posted above the company is better known as Advanced Four Wheel drive systems. Their specialty is doing 4 wheel drive conversions, mostly on vans and ambulances, but they also do all kinds of axle work.
When I dropped the FJ off, which the owner was nice enough to meet me there on a Saturday so I didn't have to take work off, he took me for a tour of the shop, and they had tons and tons of axles laying around, plus thay had 3 FJ40's they were working on too.
The owner Randy and his son(who owns a FJ40) both seem like great guys, and are very knowledgeable about the type of work they do!