I am rebuilding mine, it is my first time opening up a tranny, hopefully it'll be good though. I chose a $700 tranny to mess around with too. Ahh well.
The hard part comes from measuring, as everything has to be in a pin-point exact location, mechanics of it are easy though. Are you trying to replace syncos or install and LSD? For the differentials you need to shim the hypoid gear so that it has proper backlash, otherwise you can mess up the ring and pinion. The bearing are also a part to be careful about, as if one of them is too tight and end up locking up, it will take the case with it too.
Just take your time, do everything as a book says (buy a good repair manual, get printouts from the dealership), and you'll be fine.
Have fun.


**And no, it's not like doing a swap. Changing an engine is unbolting bolts and pluging in connections, there is no percision involved. If something is a little off, then you can easily and very efficiently ruin the tranny.