I just put in an 04 LQ9 in my 06 LJ Rubicon and I kept my NSG370 6 speed. Used Novak adapter for the tranny to engine. I was able to keep my transmission in its stock location by pounding in the corners of the firewall, watch out for your heater core when doing this. Ask me how I know. This allowed me to keep both driveshafts, engine skid did not need to modified, and left plenty of room for electric fan. You will be happy if you switch.
2006 LJ Rubicon 6-speed manual; Warn Rok Krawler Front and Rear Bumper; WARN 8000m winch; OME Long Travel Nitro Shocks; OME 933 Front Coils; OME 949 Rear Coils, Rokmen engine, tranny, gas tank skid; Metal Cloak front and rear fenders; Rokmen upper and lower control arms; Kilby steering box skid; Currie steering; Currie Anti-Rock; Trail Ready HD 17" Beadlocks; Goodyear MTR 35x12.50R17; Rock Hard Sports cage and rocker slider; Corbeau XRS seats; RCV Performance front axle; ARB 35 spline rear locker; ARB CKMTA dual compressor; GM LQ9 6.0l