I been noticing that my auto trans in my 96, 16valve is acting funny.  Sometimes it works just fine and sometimes it doesn't want to shift.  It will run thru 1st gear and it wont shift into 2nd or 3rd, sometimes I have to mess with the gas pedal to shift and yesterday it slipped going into 2nd.

I've never messed with a Tracker auto.  I know with Chevy's they have a vacuum modulator that is known to cause this same problem so I was wondering if there was something I could try with my Tracker. 

Oh yea, fluid is clean and full.

  Can't speak for the 96 model, but both my 92 Kick and 95 Tracker autos have vacuum modulators.  I replaced the one on the 92 quite some time ago with new one from OReilly's.  I don't remember it being very expensive.

Clean the valve body, this happens after
changing the fluid, it seems to wash some
loose junk into the workings of the body.

when I first got my tracker, the tranny was not going into gear, it would rev and not go when in drive, I know the tranny had just been flushed/filled prior to purchase, so I was at a loss as to what to try. I threw a bottle of seafoam auto tranny treatment in there, and it straightened it right out, been fine ever since....

I'm gonna try the vacuum modulator.  Inexpensive.  I havent changed the fluid, it still looks clean, but I will drop the pan and see how it looks.

I threw a bottle of seafoam auto tranny treatment in there

Is that a leave in treatment?  Or a have flushed soon after?

Check the simple things first,check the hose connections and check condition of hose..