I have a 1997 Tracker 4dr 4x4 with a 3 speed automatic ( 1 2 drive ) and 1.6 I4, 16v engine that is locked up. I have access to a 1995 1.6 I4 16v engine, 5 speed transmission with transfer case, and an ECM from a 1996 Tracker 2dr 5speed 4x4. I would like to convert 1997 Tracker 4dr to a 5 speed using the 1995 Tracker engine, transmission, and transfer case. What do I need to do to make this happen? Thanks for any and all help.

Just make sure you get all the emissions garbage off your obd2 engine and get it on to the obd1 motor you are going to put in.. if something is differant you are going to be throwing a cel, if you have emissions testing you will fail, and most of the time if you have a cel your motor will run rich and you will lose mpg and performance

The only difference between the 95 and 96 engine other then the intake is the oil pump and oil pan.  The hard part is gong to be installing a clutch assembly so you can use the 5 speed transmission.  The drive shaft might also be different, not sure about that though.

You will probably need the gears front and rear from the 5 speed also. Most automatics have higher gearing in the diffs unless they have been changed out for the lower gears in the past.

I have a 1997 Tracker 4dr 4x4 with a 3 speed automatic ( 1 2 drive ) and 1.6 I4, 16v engine that is locked up. I have access to a 1995 1.6 I4 16v engine, 5 speed transmission with transfer case, and an ECM from a 1996 Tracker 2dr 5speed 4x4. I would like to convert 1997 Tracker 4dr to a 5 speed using the 1995 Tracker engine, transmission, and transfer case. What do I need to do to make this happen? Thanks for any and all help.

First off, unless someone swapped it in, your 97 4 door doesn't have a 3 speed auto.  The only 4 door to have a 3 speed auto was the 91s.  Yours should have a 4 speed auto.
Secondly, there are more differences between 95 and 96 and newer engine setups than just the intake, oil pump and oil pan.  95 and older are OBD1, 96 and up are OBD2.....so that means the distributor is different, the wiring and engine control wiring  and ECM is different.  The best way to use the 95 engine in yours is to take your distributor, intake, oil pump, lower timing belt pulley and oil pan and put on the 95.  You should be able to keep your ECM and wiring with the 5 speed tranny (in my experience, auto trannys don't care if you run a 5 speed behind them, they don't know the difference).  There is some wiring that runs to the 95 tranny and tcase, but the 97 wiring should be compatible, or you should be able to splice a couple of wires and get it to work.  It is just for the 4x4 indicator light and back up lights.
Use your tcase on the 5 speed tranny.  It will bolt up fine.  Plus, the 97 tcases use a different spline on the output shaft.  But, if you do have a 4 speed auto and are swapping to a 5 speed, you will have to get new front and rear driveshafts, since they are not the same length between 4 speed autos and 5 speeds.  But if you do in fact have a 3 speed auto in it, then you can reuse the driveshafts, since the 3 speed auto and 5 speed use the same length driveshafts.
Oh, and on the axle gearing.  All 4 doors have 5.12 gears no matter what tranny they had.  The exception to that are the 91 4 doors, which had either 4.62 or 5.38 gears, depending on whether they had the 3 speed auto tranny or the 5 speed manual tranny (91s were the only 4 doors to have the 1.6 8V engine in them...that is why they were geared differently).

Ah, I forgot that the distributor changed on the different engines.  But the distributor housing is the same so you can just swap your distributors over.

I put a 95 motor into my 96.  I had to swap the intake, exhaust, distributor, and that water tube that comes out the back of the water pump.

The tube on the back of the water pump was the real pain, as it was unexpected and I had to find a gasket/seal for it.