So i just bought this and It's a project. I've been a jeeper most of my life but have built a sammy and a few trackers in the past. This has a really neat lift I believe its maybe the only one produced. I haven't figured it out yet but its going be fun as heck when I get it ironed out?
1st. Axles are not stock but don't know what they are.
2nd. rear end walks while flexed
3rd aluminum front diff
4th stock t/case
5th front suspension is stiff 400lbs coils on coil overs

more pic's

You need to post some more close up and detailed photos of the suspension, front and rear, so we can dissect this thing!

Chances are the rear end is walking when flexed because it looks like the suspension links are stock length. They are pretty short and with that much lift they are going to be very far from the horizontal angle they would be if not lifted. The more angle to them, the more dramatic the change in wheelbase as the suspension cycles.

The aluminum diff can be replaced with a steel one out a V6/manual trans GV or XL7. Or a solid front axle.

The stock t-case can be upgraded with low-range gears from TrailTough or Calmini. I think 4.24:1 is the only option, but it will improve the crawl-ability of the truck by a hundred-fold. There are other options that involve using a different tranny/transfer case combo, like doubling up a 2wd Tracker tranny to a Sammy t-case which has more options for gearing and also has high-range reduction, or doubling up a Tracker t-case to a Toyota t-case, etc, or installing an underdrive box between the tranny and t-case, etc. The trickiest thing with these types of setups is the overall length of the package and the short wheelbase of the vehicle can lead to driveline vibrations and other related complications. But you're a Jeep guy so you probably already know all about that.

I'm sure it wouldn't be too hard to find a set of softer springs for those coilovers online. At least you know what's in there now so you have a baseline to tune from. The big question is, do you want to spend money "perfecting" that IFS or just do a straight axle swap and have something reliable if somewhat less side-by-side-like in high-speed performance?

As for the rear axle suspension yes I know the angles of the arms are all wrong for any type of real wheeling. The transfer case, I believe It will be getting dual yota set up with the adapter from low range.  The front IFS system is going to stay! I disagree with anyone saying straight is more reliable they both break. Straight axles are simpler it get right and easier to maintain.
  I will be posting more pic's soon.
  The plan right now is to lower the diff.dual rate coils 400 and 200/250 haven't done the math yet. The suspensions is cranked to the max on the front in order to clear the tires. (34-10.50 ATV terminators are for sell $850) I'm still not for sure which models have the same mounts as my 2000 tracker to source a steel diff from.
  I really have not looked at this much yet, I have been busy with work and other projects. I am wondering will manual lock-outs bolt right up or if the is something different from auto hubs to manual? Has anyone did the math what angle will a CV live at? My son figures the axles are 43 degrees sitting at rest. Of course that's is extreme.  At a quick glance we figure 21.7 degrees at rest can be obtained relatively simply.

I'm still not for sure which models have the same mounts as my 2000 tracker to source a steel diff from.

Presumably you're referring to which Suzuki models - as far as I know, all the Sidekick, Vitara & Grand Vitara front axle housings can interchange, as can XL-7s prior to 2003 - the axle mounts are where the difference lies, and those can be unbolted and the ones you have now fitted - steel axles were fitted to the XL-7s and the V6 Grand Vitaras with manual transmissions.

I am wondering will manual lock-outs bolt right up or if the is something different from auto hubs to manual?

Auto hubs?  That model Tracker never had an auto hub option from the factory - the freewheel mechanism is built into the differential and a splined cap connects the axle to the hub - you can unbolt the splined cap and bolt a manual free wheel hub in it's place, but you will still need to bypass the freewheel mechanism in the differential - options are lock it engaged either by welding or with nylon ty-raps, or fit a non freewheel differential from an earlier model.

Thank You. For the info, So what I need is a Steel housing from a gv, or xl-7 up to 2003? For the non actuated center section is there a steel unit or will the gears etc swap over to a later unit. Eliminating the air actuator and running lockouts is the goal. 
 

more pic's

pics

Eliminating the air actuator and running lockouts is the goal.

There used to be an article here on SOTF (Shift On The Fly) delete detailing what was needed to get rid of the air actuator - the diff assembly from the earlier Sidekicks swaps in to the center section and can accept the ring gear from the air actuated diff assembly, the tricky part is that the air diff is offset by a few tenths of an inch so you have to fiddle with the axles - I suspect with the front end on your vehicle the way it is, you may be looking at custom machining on the axles.

I am going to be digesting those photo's for a some time.  Thanks.
With the angles on your CV's, and the fact that they are turning all the time, it is hard to imagine that they are functional.  You need to add a diff drop to your list of things to do.  It is the only way to decrease those angles and still maintain that lift.  I do not know what the safe angles are, but I am running on 33's with a diff drop and 14.5" to bottom of frame, and my CV's are holding up with 185 hp.
What area are you in?

I'm just out side of St Louis Mo

Any updates?

We've been dealing with a serious condition in family, plus very busy summer with very little $$ to spend on tracker hoping to get into shop and start modify soon. new years is goal for maiden wheeling trip.