Ok, this might confuse some but ill try and explain the best way i can.
I have a 95 Tracker frame (4wd) and 16v motor (auto) that i put a 91 tracker body on (came off a 2wd standard and smaller motor) Will i have to change out my WHOLE wiring harness or will the current one in the 91 tracker match up to the 95 tracker? I have heard i have to change the whole thing with me going to a 4wd and a bigger motor and auto tranny. Any help would be greatly appreciated! Thanks so much. 

The only part that you will be able to reuse is the part that runs from the drivers side kickpanel back to the rear (tail lights, fuel tank, etc.).  For the rest, it would just be easier just to swap it all out.  It really isn't too bad to do.  Just remove the dash first and pay attention to how it comes out, so you can put it back in and route it correctly.  You will probably need to use the 95 instrument cluster with the 95 harness too.  There are a few variations of clusters and it would be easier to just use the 95, to make sure it is compatible.

As Skyhiranger points out the wiring swap is a merge of the systems in that he is utilizing body wiring which will probably not use same connectors.  In which case what I have below also applies.  The instrument clusters are not same size & shape, so instrument cluster swap will take a new instrument cluster housing to install one.  Pulling the dash as he points says is easier than laying on your back, contorted, reaching up & between to work.  It is also easier to neatly make wiring changes.
 (I wish I had pulled dash when I made my swap.)
Take lots of photo's of both wiring as it comes out, they are much better than memory.


They can be merged.  You need to be able to read (understand) wiring diagrams, splice wires (solder for best results, or use aircraft wire connectors), have both FSM's wiring dagrams, have time and patience.  It is best to have the donor vehicle available.  As the systems are very close to the same, it should not be that hard .
I have merged a 2005 2.7 5 speed automatic into '93 Tracker 5 speed manual.  This year I spent a month chasing loose wiring connections & broken grounds. I only had motor/tranny wiring & had to makeup connections into Tracker connectors.
Most wiring color codes are the same, which makes it easier.  I do not think it would be as hard as changing out all vehicle wiring, but then with a complete change out anyone could use FSM wiring diagrams to know what should be where.  Electronic speed signals to ECM are different, and would require (possibly changing speedo in dash, new wire - research to understand). 

Then again Trail Tough or Low Range Offroad, may have/do a plug & play wiring loom for you as this is a popular change out.

I am pretty sure the intrument clusters are all the same size and shape from 89-95 on trackicks.
There should be no splicing/taping/soldering/etc. involved, if the whole wiring harness (except for the rear section) is replaced.  And the rear section should be plug and play between the 8V and 16V harnesses.
I have swapped wiring harnesses before between 89-95 trackicks and it really isn't hard at all.  Especially if you have the dash and drivetrain out, so you can see what you are doing and where/how the wires route.

where does it disconnect from the front and rear sections?

where does it disconnect from the front and rear sections?

At the drivers side kickpanel.

and my 16v wiring harness should just plug into it?? Im putting the 95 tracker whole dash (speedo,ac,radio,ect.) in the 91 also, will it fit/work?

and my 16v wiring harness should just plug into it?? Im putting the 95 tracker whole dash (speedo,ac,radio,ect.) in the 91 also, will it fit/work?

The wiring that goes into the drivers kickpanel is not 8V or 16V specific wiring.  They both have and use those same wires.  So I am pretty sure the connectors are the same and the wiring is in the same spots in the connector.  I think it is a blue connector, if I am remembering correctly.
I believe that the whole dash will interchange as well.  There were some pedal changes between the early years and the later years, but I don't recall that it affects the dash fitament.