Hi, in high 2nd and low 3rd my Sammy starts vibrating, the 4wd shifter can be seen vibrating as well, this all 
goes away once I start speeding up, but starts again in the same gears when stopping

Could just be a broken Tranny/Trans Case mount? Is there a "grinding" sound associated with the vibration?

Sounds like mounts to me....

You might also want to check the u-joints in your intermediate shaft between the transsmission and the transfer case, also make sure the bolts are tight.

I second the U-joint check... And maybe the t-case mounting arms if the U-joints check out ok...

I'll check or out, thanks so much

check all the mounts, check that your drive shafts are all tight and ALL the bolts are there and then if all else fails then take the shafts off and check the joints. You can check them on the zuke but you will only get a good feel off the zuke.

I'd guess that it's a t-case mount. Get under and push up on the t-case. The rear mount on the tranny is very comon to break and it really sucks. There are upgrades for sale out there.

You can get away with just using a bolt through a rubber washer/bushing. This is not good at high speed and you'll probably get some vibes but will get you out of a bind. IF you got a karting track near by they probably have rubber mounts that would work great. I've changed a few zukes and none have broken yet.

If you find a bad u-joint then just change both on that shaft. Remember to make sure that it moves free when it's all clipped into place. IF its stiff then tap on the shaft until it moves real good. Another trick I learnt a long time ago was that some places offer lifetime warranty....like Canadian Tire. I wait a few months and bring in the old u-joint cross to get a replacement. most of the staff at this store either has no clue or just doens't care and will give me new joints just like that and given a life time warranty means that you can just use the same receipt over and over again. I've got 10 spare joints in the shed right now.

I rebuilt the tranny(for longevity sake), and it still vibrates off and on. Took it to Pep Boys, says all the Mounts/Joints are fine, they cannot find anything wrong with it, say bring it back when it starts doing it again :'(

Either somethings off balanace, or find a new shop.

Yours trans if fine, I would look else where for the culprit.

Bryce

You might want to makes sure that the driveshaft was put back together properly.  If it is not aligned properly it could be causing your problems.