Wow.  I didn't know so many people wanted to do the same thing as me.  Okay...here's my prob/question.  I just picked up a 1997 Jeep Wrangler 4L Automatic.  I'm thinking its the same trans as everyone's here which is also broken.  I have the option of buying a whole 2006 Rubicon 6spd which was involved in a front end collision for about $2000.  If I buy the Rubicon would the Rubicon have everything I need to make the 6spd. and transfer case bolt right up to my 1997 Sport and START UP?  If not where can I get tech info on helping me with the swap.  Really want to do the swap.  Also, I'm thinking about running 38" to 40" tires!  

Before anyone asks or says anything...the chasis is a goner but everything else is in good condition.  Another reason why I want to go this route is because the Rubicon's interior is still perfect condition as opposed to my Sport.  So I will be using more parts from the wrecked Rubi than just the tranny.  

If I were you I'd scavenge every working mechanical system on it!

Your 97 is over 10 years old now and the Rubicon had some upgrades above what was stock then.  Why not just pull the entire drivetrain and transplant it....actually basically just use the frame and body from your old Jeep and everything else from the Rubicon.  That would give you better gas mileage, more HP, disc brakes, and a more rugged suspension.