I am not 100% totally positive, but I believe every Toyota factory radio (with the exception of the JBL's) is interchangable. I had one off of a Corolla or something in my 4Runner for a bit, but sold it to a guy who had an FJ and he said it mounted straight in with no modification.
The FJammer is a very nice stereo and is worth a shot. I've seen them on the FJ site going for $50 - $100. I wouldn't pay any more than that. Not because it is a bad stereo.... but because guys are willing to sell them cheap when they upgrade to a nav unit. It is a steal at $100, and to me it beats a lot of the aftermarket radios that would cost 3 to 4 times as much. I say that because it is not only a great sounding setup for the price, but it is easy to use, and it looks good since it mounts in the slot without needing spaces or any mounting kits. You will just use the mounts that are on your current stereo.
The antenna thing is the only place where you might need adapters, and that just depends on whether or not you have the dual antenna leads that come from the window. If you do then I can give you the part numbers you need to order (you can get them off of Amazon, or I even have a set that I can send you if I can find them) and they are under $20 for the two pieces and everything will most likely work perfectly. The nice thing about the FJ is that it is basically a 4Runner in disguise, so there are many parts that are interchangeable between the two.