Yes its possible they saw one side only, but only the rears were digging in. On the c clip they replaced it. I think I need to do the diff drop.my shaft on drivers side is the original gen 2 shaft so if I understand you correctly I already have the long one so reducing the angle with the diff drop is my only solution I can think of. I was bouncing down a deep sand road when I got stuck. lots of people get stuck in the spot I did because there were carpets and moving blankets left behind by others .So I am going to guess it either pulled out when I started bouncing in the whoops or with 32 psi and weight in the rear the rears dug more than the front and they missed the wheel spinning. With it working now I am left guessing. I guess I could have Brett at trail tough build me a hybrid shaft for passenger side that sticks in an extra 1/2" and I would only need one spare cv axle. Thanks for the help fellas

my shaft on drivers side is the original gen 2 shaft so if I understand you correctly I already have the long one so reducing the angle with the diff drop is my only solution I can think of.

I guess I could have Brett at trail tough build me a hybrid shaft for passenger side that sticks in an extra 1/2" and I would only need one spare cv axle. Thanks for the help fellas

I don't think I've made my point clearly, captwoody.  You probably do have the original driver side CV on your truck.  Even if they replaced the 2nd gen original CV with the CV from the 1st gen Sport... it would be the same size/type/part number of CV anyway.  The inner axle I am referring to is the axle shaft inside the axle housing that the driver's side CV bolts to with the three bolts on the flange.  This inner axle shaft is the one I think should be in question. 

You shouldn't have to have Brent build you a custom  CV shaft.  Just call the shop who did your work and ask them which inner axle shaft they used.  Or... just measure the inner axle shaft you have on hand (whichever is left over) and compare the measurement with these (as measured from the flange surface).  The first pic is the 1st gen inner axle shaft measurement  - 15 3/8ths.  The second pic is the 2nd gen inner axle shaft measurement - about 15 3/4  inch.

ok so gen 1 is the longer one. and my inner shaft is my original so its 15 3/8", and they replaced the passenger side cv axle and c clip the drivers side is original

No... my mistake, captwoody.  I mislabeled my pics in my last post.  The 1st gen inner axle shaft is the shorter of the two shafts.  I corrected my post in bold text.  My apologies.

So my point was and is that if the garage that installed your 5.12 gears onto your original 2nd gen differential then installed the Sidekick Sport housing and inner axle into your truck... then you have and are running the short inner axle instead of the longer 2nd gen axle that "works" with the 2nd gen differential.  If they  installed your 5.12 geared diff (instead of swapping gears to the newer differential), you would want the shorter 1st gen inner axle.

The ring and pinion gears are inter changeable.  It is the diff carriers difference in width (because of the design which accommodates the air actuator on the 2nd gen differential case) that causes the difference in side gear width when assembled and therefore, the need for the different length of inner axle.

I told them to use a sidekick sport 1.8l passenger cv axle but they were supposed to just swap thirds they put the 5.12 ring and pinion into my 01 housing with my SOTF.going to order drop brackets for front

OK, gotcha.

ok I now understand what you are saying. when I swapped to the 512 I used the whole front diff from the sport (aluminum housing, gears and CV axles) the brackets that are bolted on the sport front diff are 2" longer than the 2002. I didn't use them but, I did keep tem just in case I could use them in the future. so I never swapped out thirds. the aluminum (banjo) part of the diff carrier is the same from the sport to the next gen. Makes sense that the axles would be different as your tracker had the SOTF mechanism  in the way and the axle wouldn't need to travel that far in the housing

You got it, beagle-t.   IF you had knocked out that inner axle shaft from the Sidekick Sport front housing  and compared it to the original one on your Tracker, the Sport inner axle would have been shorter than the Tracker's by about 3/8ths of an inch.  Just like in the picture.

I thought that you were going to get rid of the SOTF, I guess the shop screwed up and didn't understand you. because you have locking front hubs the sotf mechanism is rendered useless and they should have just installed the front third with the 512 and used the sport inner axle and your problems would be solved ......I know sounds easy 

Exactly Beagle,When they had it apart they saw the SOTF unit they thought it was a front locker and decided oh he is going to want to keep that.if they would have called when they found it i could have told them.out here in so cal nobody is familiar with trackers.

Captwoody
 Nice looking Zuki on the table

Nice looking wheels too!  It's those random file associations. 

Darn i though i won a RC Sammy

You are close to Petroworks and I hear good things about their shop.  Have you stopped by to check them out.  Parts and service specifically for the Zuk crowd

http://www.petroworks.com/

Petroworks Off-Road Products

111 West Aviation Road

Fallbrook, CA 92028

Petroworks made me feel they were not real eager to work on gen 2  trucks. I have called them on several things,although they were willing to do my 5.12 for 1550 which was 450 more than the shop my regular mechanic recommended brothers 4x4 in Montclair