I did a big thread on the old site with pics of the locations of most of the breathers. Unfortunately it seems to have disapeared so I'll try to describe thier location to you.
Axle breathers - the top of each axle tube near the diff. One on the front one on the back.
Gear and transfer box - are at the top of the boxes, you can find them by tracing the breather pipes back to thier start. I'll tell you now, if you can fit them from under the car then you are a good un. Save yourself the hassle, remove the centre console (Dont break it, take your time), drill out the umpteen rivets holding the rubber shield down and attack them from above. You can re-rivet or use some fat self tappers to re fit it. This shield will have to come out every time you remove the gerbox, change the clutch etc so self tappers are the most logical option.
Crankcase - this needs to be drilled and tapped then have an elbow fitted to it. I havent done this and without removing the cover (Hence serpentine belt etc) I dont fancy risking it. You never know whats behind the bit you're drilling! So, remove the cover, see what your doing, fit the breather and you should be able to leave the wading plug in permantly as long as you have no oil leaks behind the cover. Either way you should probably pop the plug out every month or so just to make sure its not filling up.
Fuel tank - I dont know where this one is, sorry. I have heared it said that if your going this deep, worry about your dashboard, stereo, wristwatch etc first :)
Hope this helps, Stu.