I'd recommend the manual swap. I have an auto and a manual bimmer, and needless to say, the manual is much more fun.
You can pick up all the parts needed for the swap for around $1,250 to $1,500, and the labor is anywhere from $400 to $900, depending on where you get it done.
Rob on UB just thump his auto->manual swap a few days ago, so he could answer any questions you have about that.