So I bought a 1999 2 door 4x4 manual transmission, the other day. Looked under and saw some wetness under the real end housing.  Does it have a vent hole that may be plugged? Does that cause leaks on theses?

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When you say "wetness" under the rear end housing... are you referring to the pinion seal area.... or where the diff bolts to the axle housing... or the ends where the axle seals are located, just inside the wheels?

The axles do have a vent on the top of the axle housing (at about the 1 O'clock position when viewed from the rear).  They can become plugged, but I suspect it is more likely that the seals are worn (pinion... axle or both).  The diffs generate heat when rolling and when the diff is suddenly submerged into cool water when crossing a stream or a deep puddle in the road, the sudden cooling of submerging the warm diff into the water creates a suction that could allow water to get sucked in because of worn seals.  If the seals are good, there should be little problems with water passing by them.  If water can come in... then gear oil can leak out.

Of course, if you don't know the history of the truck and the past maintenance, it is a safe assumption the seals could be excessively worn.  It is extremely rare to find a truck with documented maintenance history.  If you find one, they are worth the additional cash you may pay for it because you know more of what you are buying.

You should drain the diff and see if it is just dark... or milky colored from water contamination.  If it is the pinion, the seal can be replaced without removing the diff if you very carefully mark all the surfaces for reference beforehand (the pinion nut full turns, number of exposed threads on the pinion, pinion position, etc).   The axles seals are fairly easy to replace as well.  If you opt to install new axle bearings, it can be done at home as well IF you have a small diameter cutting wheel to cut the old bearing collars off carefully and a standing press (at least a 12 ton) to press off the old bearing and press on the new bearings and bearing collars.  Rockauto carries the Centrix brand axle bearings that come with new bearing collars.  Some of the  axle bearings they sell don't come with new collars.  The old ones (even IF you could remove them in one piece) shouldn't be reused.

In either case, be sure to put a good bead of RTV on the back of the axle retainer plates (4 bolts secure it to the axle assembly) during assembly because water can work into the axle behind them as well.

Thanks, well I found this tracker with 119k miles on it and it doesn't look like it's seen much dirt. California car and I have the service records but I'm seeing things not mentioned. Runs great  only one small door ding on the body. New radiator and I see someone replaced the valve cover gasket recently so hoping that means someone looked at the timing belt. It's going to be a  toad on my rv hoping to do some off roading but nothing crazy. 

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My tracker also has very wet rear diff and it’s clearly not coming from the front pinion seal though.  So, not sure how that could happen or where it’s coming from.  I resealed the drain plug with goopy stuff so hope that helps. 

The second gens have a raised vent, which terminates in the cavity behind the left tail light, you need to make sure that the vent is not plugged as any expansion caused by heat will force the oil out past any opening, sealing the drain & fill plugs can result in oil being forced past the seals.