Son's 87 sammy lost the jack shaft and busted up the 5 speed tranny.   We have a 95 side kick 4 door with a 1.6 motor and 5 speed tranny with a transfercase slaved to the tranny.  Would like to put the motor and tranny in the Sammy.  What is going to be the major issues doing this.  We were originally going to just swap out the motors and may still do so.  Any info on either or to the above would help us.

In order to use the transmission out of a 4wd Tracker and have it go to the existing Samurai transfer case you will need something similar to the Kicker 1 or Kicker 3 system at http://www.ottindustries.com/gearing.htm

People have made their own without to many issues.  The alternative is to pick up a 2wd transmission for a Tracker and just use it.

You can go through Trailtough and get an adaptor to use a shortened Sami intermediate driveline with the Kick trans... You will need to widen the transmission tunnel in order to make it fit and make a crossmember for it as well...