I did a LS6 swap in my 2000 with the 5 speed, still not complete yet due to starter clearance issues. Gonna finish it in the spring. I used a 2001 2wd truck harness, couldn't find a 5 speed harness so I just got the auto. Only thing I had to do was jump the 2 wires at the park neutral switch connector so it'd start with the key.
2000 Chevy Silverado RCSB LS6 5 speed, LS6 short block, 317 heads, LS6 intake, Lunati 220/224 .575/.575 112LSA cam, Edelbrock Headers, CTS-V accessory drive, Nelson Performance Custom Tune.